Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0888/LS0888_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/6e/27ec033b0f87e3a9b18dda38d3a6e3/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0888/LS0888_tumor.bam.bai
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://natera-rnd-fsdx-dev-nextflow-scratch-01/work/6e/27ec033b0f87e3a9b18dda38d3a6e3/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:11.723 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
22:44:11.870 INFO Mutect2 - ------------------------------------------------------------
22:44:11.872 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:11.872 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:11.873 INFO Mutect2 - Executing as ?@nf-6e27ec033b0f87e3a9b18dda38d3a6e3-02ca2-qlsvz on Linux v6.12.88 amd64
22:44:11.873 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:11.873 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:11 PM GMT
22:44:11.873 INFO Mutect2 - ------------------------------------------------------------
22:44:11.873 INFO Mutect2 - ------------------------------------------------------------
22:44:11.874 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:11.874 INFO Mutect2 - Picard Version: 3.1.1
22:44:11.874 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:11.874 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:11.875 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:11.875 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:11.875 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:11.875 INFO Mutect2 - Deflater: IntelDeflater
22:44:11.875 INFO Mutect2 - Inflater: IntelInflater
22:44:11.875 INFO Mutect2 - GCS max retries/reopens: 20
22:44:11.875 INFO Mutect2 - Requester pays: disabled
22:44:11.876 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.SOlxRmCbkf/LS0888_tumor.bam.bai is older than BAM /tmp/nxf.SOlxRmCbkf/LS0888_tumor.bam
22:44:12.103 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.SOlxRmCbkf/af-only-gnomad.hg38.vcf.gz
22:44:12.209 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.SOlxRmCbkf/TST500C_manifest.bed
22:44:12.244 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:12.279 INFO Mutect2 - Done initializing engine
22:44:12.294 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
22:44:12.297 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
22:44:12.298 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:12.298 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:12.307 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
22:44:12.316 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:12.316 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:12.317 INFO IntelPairHmm - Available threads: 384
22:44:12.317 INFO IntelPairHmm - Requested threads: 4
22:44:12.317 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:12.359 INFO ProgressMeter - Starting traversal
22:44:12.360 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:23.155 INFO ProgressMeter - chr1:9724347 0.2 50 277.9
22:44:34.985 INFO ProgressMeter - chr1:11233396 0.4 110 291.7
22:44:47.727 INFO ProgressMeter - chr1:15930098 0.6 160 271.4
22:44:57.781 INFO ProgressMeter - chr1:15935420 0.8 190 251.0
22:45:10.845 INFO ProgressMeter - chr1:18746584 1.0 250 256.5
22:45:21.384 INFO ProgressMeter - chr1:26773578 1.2 310 269.5
22:45:31.648 INFO ProgressMeter - chr1:36473433 1.3 360 272.4
22:45:43.413 INFO ProgressMeter - chr1:39905878 1.5 420 276.8
22:45:54.292 INFO ProgressMeter - chr1:46260725 1.7 480 282.5
22:46:05.847 INFO ProgressMeter - chr1:64855507 1.9 540 285.5
22:46:16.426 INFO ProgressMeter - chr1:91772316 2.1 600 290.2
22:46:27.683 INFO ProgressMeter - chr1:119514436 2.3 660 292.6
22:46:39.843 INFO ProgressMeter - chr1:119948412 2.5 710 288.8
22:46:53.345 INFO ProgressMeter - chr1:156873534 2.7 770 287.0
22:47:04.918 INFO ProgressMeter - chr1:158611262 2.9 790 274.7
22:47:16.402 INFO ProgressMeter - chr1:158667896 3.1 850 277.1
22:47:27.231 INFO ProgressMeter - chr1:176163813 3.2 920 283.3
22:47:37.833 INFO ProgressMeter - chr1:204431693 3.4 990 289.1
22:47:49.033 INFO ProgressMeter - chr1:204538300 3.6 1060 293.5
22:47:59.584 INFO ProgressMeter - chr1:226071349 3.8 1120 295.7
22:48:12.499 INFO ProgressMeter - chr1:243501053 4.0 1190 297.3
22:48:22.753 INFO ProgressMeter - chr1:243613669 4.2 1220 292.3
22:48:35.030 INFO ProgressMeter - chr10:27053299 4.4 1280 292.4
22:48:45.397 INFO ProgressMeter - chr10:32031071 4.6 1330 292.3
22:48:56.182 INFO ProgressMeter - chr10:43112265 4.7 1380 291.7
22:49:07.348 INFO ProgressMeter - chr10:43116053 4.9 1410 286.8
22:49:19.271 INFO ProgressMeter - chr10:43126958 5.1 1450 283.5
22:49:30.714 INFO ProgressMeter - chr10:68573553 5.3 1490 280.8
22:49:40.900 INFO ProgressMeter - chr10:86900122 5.5 1530 279.4
22:49:54.302 INFO ProgressMeter - chr10:101770136 5.7 1600 280.7
22:50:04.819 INFO ProgressMeter - chr10:110581902 5.9 1670 284.3
22:50:15.432 INFO ProgressMeter - chr10:113160617 6.1 1720 284.2
22:50:27.849 INFO ProgressMeter - chr10:121482718 6.3 1760 281.2
22:50:39.622 INFO ProgressMeter - chr10:121577835 6.5 1810 280.4
22:50:50.880 INFO ProgressMeter - chr11:64360475 6.6 1890 284.6
22:51:01.481 INFO ProgressMeter - chr11:69644122 6.8 1970 288.9
22:51:12.709 INFO ProgressMeter - chr11:69700941 7.0 2020 288.3
22:51:23.905 INFO ProgressMeter - chr11:69771328 7.2 2060 286.4
22:51:35.324 INFO ProgressMeter - chr11:69808267 7.4 2100 284.4
22:51:45.545 INFO ProgressMeter - chr11:69812287 7.6 2120 280.7
22:51:57.233 INFO ProgressMeter - chr11:76496216 7.7 2170 280.1
22:52:07.625 INFO ProgressMeter - chr11:77344065 7.9 2210 279.0
22:52:22.878 INFO ProgressMeter - chr11:77423651 8.2 2250 275.2
22:52:36.242 INFO ProgressMeter - chr11:101128888 8.4 2320 276.3
22:52:46.306 INFO ProgressMeter - chr11:108257505 8.6 2370 276.7
22:53:00.277 INFO ProgressMeter - chr11:118472180 8.8 2450 278.5
22:53:12.902 INFO ProgressMeter - chr11:118503641 9.0 2500 277.5
22:53:24.919 INFO ProgressMeter - chr11:119299742 9.2 2550 276.9
22:53:38.477 INFO ProgressMeter - chr11:125675449 9.4 2600 275.6
22:53:49.117 INFO ProgressMeter - chr11:128461749 9.6 2620 272.6
22:54:00.547 INFO ProgressMeter - chr11:128813136 9.8 2670 272.4
22:54:11.743 INFO ProgressMeter - chr12:916743 10.0 2730 273.3
22:54:24.188 INFO ProgressMeter - chr12:4430742 10.2 2790 273.6
22:54:34.689 INFO ProgressMeter - chr12:6570674 10.4 2840 273.8
22:54:46.247 INFO ProgressMeter - chr12:6602422 10.6 2890 273.6
22:55:00.001 INFO ProgressMeter - chr12:11857916 10.8 2930 271.4
22:55:13.669 INFO ProgressMeter - chr12:11863287 11.0 2970 269.5
22:55:25.463 INFO ProgressMeter - chr12:11868606 11.2 3000 267.4
22:55:35.746 INFO ProgressMeter - chr12:18562870 11.4 3060 268.7
22:55:46.583 INFO ProgressMeter - chr12:31804367 11.6 3120 269.7
22:55:58.698 INFO ProgressMeter - chr12:49028826 11.8 3180 270.1
22:56:09.478 INFO ProgressMeter - chr12:49034408 12.0 3210 268.6
22:56:19.842 INFO ProgressMeter - chr12:49042739 12.1 3250 268.0
22:56:30.572 INFO ProgressMeter - chr12:50086662 12.3 3310 269.0
22:56:42.150 INFO ProgressMeter - chr12:56097043 12.5 3380 270.5
22:56:52.236 INFO ProgressMeter - chr12:57093890 12.7 3420 270.0
22:57:02.527 INFO ProgressMeter - chr12:57746367 12.8 3470 270.3
22:57:13.508 INFO ProgressMeter - chr12:68835563 13.0 3550 272.7
22:57:23.691 INFO ProgressMeter - chr12:111418144 13.2 3600 273.0
22:57:35.612 INFO ProgressMeter - chr12:120993518 13.4 3670 274.1
22:57:46.579 INFO ProgressMeter - chr12:132659377 13.6 3720 274.1
22:57:56.825 INFO ProgressMeter - chr13:20988731 13.7 3770 274.4
22:58:07.598 INFO ProgressMeter - chr13:26382812 13.9 3840 275.8
22:58:18.128 INFO ProgressMeter - chr13:28357552 14.1 3900 276.7
22:58:28.834 INFO ProgressMeter - chr13:28387094 14.3 3920 274.6
22:58:39.951 INFO ProgressMeter - chr13:32329441 14.5 3970 274.6
22:58:50.790 INFO ProgressMeter - chr13:32354103 14.6 4010 273.9
22:59:00.887 INFO ProgressMeter - chr13:48473358 14.8 4080 275.5
22:59:12.242 INFO ProgressMeter - chr13:102401469 15.0 4160 277.4
22:59:22.352 INFO ProgressMeter - chr13:113304396 15.2 4230 278.9
22:59:33.147 INFO ProgressMeter - chr14:35402599 15.3 4280 278.9
22:59:43.367 INFO ProgressMeter - chr14:37592842 15.5 4330 279.1
22:59:54.065 INFO ProgressMeter - chr14:68411422 15.7 4390 279.7
23:00:04.743 INFO ProgressMeter - chr14:95096271 15.9 4430 279.1
23:00:15.986 INFO ProgressMeter - chr14:102085870 16.1 4480 278.9
23:00:26.978 INFO ProgressMeter - chr15:34346978 16.2 4530 278.9
23:00:39.356 INFO ProgressMeter - chr15:34357683 16.4 4560 277.2
23:00:51.570 INFO ProgressMeter - chr15:41742544 16.7 4610 276.8
23:01:03.128 INFO ProgressMeter - chr15:49430215 16.8 4660 276.6
23:01:14.132 INFO ProgressMeter - chr15:73703835 17.0 4730 277.8
23:01:25.684 INFO ProgressMeter - chr15:88136592 17.2 4780 277.6
23:01:36.708 INFO ProgressMeter - chr15:90754809 17.4 4850 278.6
23:01:47.625 INFO ProgressMeter - chr15:92984328 17.6 4910 279.2
23:01:58.031 INFO ProgressMeter - chr15:98935034 17.8 4960 279.3
23:02:08.791 INFO ProgressMeter - chr16:2082434 17.9 5020 279.8
23:02:19.190 INFO ProgressMeter - chr16:3589939 18.1 5100 281.6
23:02:30.897 INFO ProgressMeter - chr16:3728707 18.3 5140 280.7
23:02:42.992 INFO ProgressMeter - chr16:9764412 18.5 5200 280.9
23:02:53.997 INFO ProgressMeter - chr16:23622967 18.7 5260 281.4
23:03:05.189 INFO ProgressMeter - chr16:50796322 18.9 5320 281.8
23:03:16.502 INFO ProgressMeter - chr16:68811682 19.1 5380 282.1
23:03:29.433 INFO ProgressMeter - chr16:72794497 19.3 5420 281.1
23:03:41.913 INFO ProgressMeter - chr16:72798274 19.5 5450 279.6
23:03:53.181 INFO ProgressMeter - chr16:80072427 19.7 5490 279.0
23:04:03.234 INFO ProgressMeter - chr16:89280268 19.8 5550 279.6
23:04:14.064 INFO ProgressMeter - chr16:89284799 20.0 5580 278.6
23:04:24.683 INFO ProgressMeter - chr17:7313566 20.2 5660 280.1
23:04:35.258 INFO ProgressMeter - chr17:7678405 20.4 5710 280.2
23:04:46.794 INFO ProgressMeter - chr17:16064073 20.6 5790 281.4
23:04:57.355 INFO ProgressMeter - chr17:17222585 20.7 5850 281.9
23:05:08.597 INFO ProgressMeter - chr17:31330294 20.9 5920 282.7
23:05:19.184 INFO ProgressMeter - chr17:39471526 21.1 5990 283.7
23:05:29.895 INFO ProgressMeter - chr17:39719789 21.3 6050 284.1
23:05:40.063 INFO ProgressMeter - chr17:40411352 21.5 6120 285.2
23:05:51.713 INFO ProgressMeter - chr17:43057050 21.7 6210 286.8
23:06:03.658 INFO ProgressMeter - chr17:43093909 21.9 6260 286.4
23:06:15.310 INFO ProgressMeter - chr17:43532189 22.0 6310 286.2
23:06:26.499 INFO ProgressMeter - chr17:43540914 22.2 6360 286.0
23:06:36.603 INFO ProgressMeter - chr17:43544213 22.4 6380 284.8
23:06:46.995 INFO ProgressMeter - chr17:48734639 22.6 6430 284.8
23:06:58.823 INFO ProgressMeter - chr17:59899825 22.8 6490 285.0
23:07:09.062 INFO ProgressMeter - chr17:60656768 22.9 6550 285.5
23:07:20.542 INFO ProgressMeter - chr17:65536441 23.1 6610 285.7
23:07:30.834 INFO ProgressMeter - chr17:80846567 23.3 6670 286.2
23:07:41.119 INFO ProgressMeter - chr18:41970418 23.5 6740 287.1
23:07:53.695 INFO ProgressMeter - chr18:44953204 23.7 6790 286.6
23:08:03.961 INFO ProgressMeter - chr18:63317952 23.9 6860 287.5
23:08:15.484 INFO ProgressMeter - chr19:2227737 24.1 6950 289.0
23:08:26.869 INFO ProgressMeter - chr19:5223287 24.2 7030 290.0
23:08:38.393 INFO ProgressMeter - chr19:10139674 24.4 7100 290.6
23:08:48.921 INFO ProgressMeter - chr19:10986576 24.6 7170 291.4
23:08:59.986 INFO ProgressMeter - chr19:14517047 24.8 7240 292.0
23:09:10.263 INFO ProgressMeter - chr19:15186876 25.0 7290 292.0
23:09:21.796 INFO ProgressMeter - chr19:17832788 25.2 7360 292.6
23:09:34.774 INFO ProgressMeter - chr19:29816213 25.4 7430 292.8
23:09:45.632 INFO ProgressMeter - chr19:35725477 25.6 7500 293.5
23:09:57.047 INFO ProgressMeter - chr19:40240635 25.7 7570 294.0
23:10:11.892 INFO ProgressMeter - chr19:41260239 26.0 7640 293.9
23:10:21.947 INFO ProgressMeter - chr19:42293933 26.2 7690 294.0
23:10:32.480 INFO ProgressMeter - chr19:45370474 26.3 7760 294.7
23:10:44.159 INFO ProgressMeter - chr19:50402041 26.5 7830 295.1
23:10:56.085 INFO ProgressMeter - chr2:15938560 26.7 7890 295.2
23:11:06.639 INFO ProgressMeter - chr2:15950395 26.9 7940 295.1
23:11:16.715 INFO ProgressMeter - chr2:25274939 27.1 7990 295.1
23:11:27.896 INFO ProgressMeter - chr2:25771438 27.3 8030 294.6
23:11:42.898 INFO ProgressMeter - chr2:29225244 27.5 8080 293.7
23:11:53.720 INFO ProgressMeter - chr2:29320835 27.7 8110 292.9
23:12:04.111 INFO ProgressMeter - chr2:42317425 27.9 8160 292.9
23:12:17.315 INFO ProgressMeter - chr2:47414382 28.1 8200 292.0
23:12:28.177 INFO ProgressMeter - chr2:47806202 28.3 8240 291.5
23:12:43.457 INFO ProgressMeter - chr2:96253997 28.5 8310 291.4
23:12:54.294 INFO ProgressMeter - chr2:108763983 28.7 8380 292.0
23:13:06.835 INFO ProgressMeter - chr2:111126956 28.9 8430 291.6
23:13:18.607 INFO ProgressMeter - chr2:111150077 29.1 8450 290.3
23:13:28.608 INFO ProgressMeter - chr2:113223598 29.3 8480 289.7
23:13:46.529 INFO ProgressMeter - chr2:113227355 29.6 8510 287.8
23:13:58.578 INFO ProgressMeter - chr2:113231859 29.8 8540 286.9
23:14:09.238 INFO ProgressMeter - chr2:113234838 29.9 8560 285.8
23:14:20.227 INFO ProgressMeter - chr2:140238150 30.1 8620 286.1
23:14:30.276 INFO ProgressMeter - chr2:140534019 30.3 8680 286.5
23:14:41.970 INFO ProgressMeter - chr2:141254520 30.5 8740 286.6
23:14:52.541 INFO ProgressMeter - chr2:189818015 30.7 8800 286.9
23:15:02.750 INFO ProgressMeter - chr2:197420376 30.8 8870 287.6
23:15:14.037 INFO ProgressMeter - chr2:211788023 31.0 8940 288.1
23:15:26.680 INFO ProgressMeter - chr2:222201363 31.2 8990 287.8
23:15:37.304 INFO ProgressMeter - chr2:222206732 31.4 9020 287.1
23:15:50.169 INFO ProgressMeter - chr2:222212583 31.6 9060 286.4
23:16:04.723 INFO ProgressMeter - chr2:222217156 31.9 9090 285.2
23:16:15.721 INFO ProgressMeter - chr2:222298855 32.1 9130 284.8
23:16:26.257 INFO ProgressMeter - chr2:238654994 32.2 9180 284.8
23:16:38.866 INFO ProgressMeter - chr20:32435152 32.4 9240 284.8
23:16:50.332 INFO ProgressMeter - chr20:37403169 32.6 9300 285.0
23:17:02.406 INFO ProgressMeter - chr20:42885805 32.8 9370 285.4
23:17:14.051 INFO ProgressMeter - chr20:53582159 33.0 9420 285.2
23:17:24.143 INFO ProgressMeter - chr20:58909747 33.2 9470 285.3
23:17:36.455 INFO ProgressMeter - chr21:38383656 33.4 9530 285.3
23:17:46.501 INFO ProgressMeter - chr21:41470646 33.6 9570 285.1
23:18:03.023 INFO ProgressMeter - chr21:41492061 33.8 9600 283.7
23:18:13.727 INFO ProgressMeter - chr21:41500145 34.0 9630 283.0
23:18:24.165 INFO ProgressMeter - chr21:41503565 34.2 9650 282.2
23:18:35.409 INFO ProgressMeter - chr21:42186850 34.4 9680 281.5
23:18:45.532 INFO ProgressMeter - chr22:21867320 34.6 9750 282.2
23:18:58.727 INFO ProgressMeter - chr22:23291618 34.8 9790 281.5
23:19:09.395 INFO ProgressMeter - chr22:28721603 35.0 9860 282.1
23:19:23.116 INFO ProgressMeter - chr22:29286153 35.2 9930 282.3
23:19:33.867 INFO ProgressMeter - chr22:33163485 35.4 9980 282.3
23:19:44.892 INFO ProgressMeter - chr22:41177116 35.5 10040 282.5
23:19:56.135 INFO ProgressMeter - chr3:10088447 35.7 10100 282.7
23:20:07.851 INFO ProgressMeter - chr3:12355775 35.9 10150 282.5
23:20:23.186 INFO ProgressMeter - chr3:12360633 36.2 10180 281.4
23:20:35.047 INFO ProgressMeter - chr3:12366742 36.4 10220 280.9
23:20:47.575 INFO ProgressMeter - chr3:12372884 36.6 10260 280.4
23:21:01.390 INFO ProgressMeter - chr3:12376111 36.8 10280 279.2
23:21:11.768 INFO ProgressMeter - chr3:12604214 37.0 10330 279.3
23:21:22.722 INFO ProgressMeter - chr3:37020351 37.2 10390 279.5
23:21:33.148 INFO ProgressMeter - chr3:47103344 37.3 10450 279.8
23:21:43.623 INFO ProgressMeter - chr3:49686307 37.5 10500 279.8
23:21:54.555 INFO ProgressMeter - chr3:52403136 37.7 10560 280.1
23:22:05.762 INFO ProgressMeter - chr3:69937820 37.9 10630 280.5
23:22:16.067 INFO ProgressMeter - chr3:89210158 38.1 10690 280.9
23:22:26.282 INFO ProgressMeter - chr3:135179858 38.2 10750 281.2
23:22:37.931 INFO ProgressMeter - chr3:138665034 38.4 10810 281.3
23:22:49.170 INFO ProgressMeter - chr3:142498658 38.6 10880 281.8
23:22:59.483 INFO ProgressMeter - chr3:179151522 38.8 10950 282.3
23:23:10.736 INFO ProgressMeter - chr3:182963990 39.0 11010 282.5
23:23:25.277 INFO ProgressMeter - chr3:186047988 39.2 11060 282.0
23:23:35.802 INFO ProgressMeter - chr3:189872857 39.4 11120 282.3
23:23:46.658 INFO ProgressMeter - chr4:1795374 39.6 11190 282.8
23:23:57.077 INFO ProgressMeter - chr4:20541451 39.7 11260 283.3
23:24:08.559 INFO ProgressMeter - chr4:54258767 39.9 11320 283.4
23:24:20.096 INFO ProgressMeter - chr4:54683213 40.1 11370 283.3
23:24:35.564 INFO ProgressMeter - chr4:54732108 40.4 11400 282.3
23:24:47.664 INFO ProgressMeter - chr4:65331967 40.6 11450 282.1
23:24:59.300 INFO ProgressMeter - chr4:80285644 40.8 11520 282.5
23:25:09.531 INFO ProgressMeter - chr4:105237353 41.0 11570 282.5
23:25:21.238 INFO ProgressMeter - chr4:105272913 41.1 11610 282.2
23:25:31.427 INFO ProgressMeter - chr4:142160356 41.3 11670 282.4
23:25:42.221 INFO ProgressMeter - chr4:186597138 41.5 11730 282.7
23:25:53.710 INFO ProgressMeter - chr4:186620683 41.7 11770 282.3
23:26:04.616 INFO ProgressMeter - chr4:186709532 41.9 11810 282.1
23:26:15.899 INFO ProgressMeter - chr5:38949710 42.1 11870 282.2
23:26:27.504 INFO ProgressMeter - chr5:44361662 42.3 11950 282.8
23:26:37.800 INFO ProgressMeter - chr5:56885930 42.4 12000 282.9
23:26:48.831 INFO ProgressMeter - chr5:80854297 42.6 12080 283.5
23:26:59.766 INFO ProgressMeter - chr5:112839013 42.8 12150 283.9
23:27:10.784 INFO ProgressMeter - chr5:122423497 43.0 12190 283.7
23:27:22.531 INFO ProgressMeter - chr5:138827598 43.2 12260 284.0
23:27:34.351 INFO ProgressMeter - chr5:149507006 43.4 12320 284.1
23:27:45.627 INFO ProgressMeter - chr5:150121878 43.6 12380 284.2
23:27:55.738 INFO ProgressMeter - chr5:150405162 43.7 12430 284.3
23:28:09.434 INFO ProgressMeter - chr5:177090759 44.0 12490 284.2
23:28:21.772 INFO ProgressMeter - chr5:177191882 44.2 12530 283.8
23:28:31.894 INFO ProgressMeter - chr5:177294416 44.3 12570 283.6
23:28:43.248 INFO ProgressMeter - chr5:180631680 44.5 12640 284.0
23:28:54.017 INFO ProgressMeter - chr6:20481556 44.7 12710 284.4
23:29:04.393 INFO ProgressMeter - chr6:26270972 44.9 12780 284.8
23:29:17.528 INFO ProgressMeter - chr6:30704051 45.1 12810 284.1
23:29:28.129 INFO ProgressMeter - chr6:32200829 45.3 12860 284.1
23:29:38.576 INFO ProgressMeter - chr6:33320378 45.4 12910 284.1
23:29:49.269 INFO ProgressMeter - chr6:41999550 45.6 12990 284.8
23:30:01.078 INFO ProgressMeter - chr6:106105386 45.8 13070 285.3
23:30:11.606 INFO ProgressMeter - chr6:117318219 46.0 13120 285.3
23:30:23.603 INFO ProgressMeter - chr6:117322233 46.2 13150 284.7
23:30:34.005 INFO ProgressMeter - chr6:117327035 46.4 13180 284.3
23:30:44.835 INFO ProgressMeter - chr6:117332974 46.5 13220 284.0
23:30:57.948 INFO ProgressMeter - chr6:117338994 46.8 13260 283.6
23:31:08.675 INFO ProgressMeter - chr6:135189789 46.9 13310 283.6
23:31:18.981 INFO ProgressMeter - chr6:135206087 47.1 13350 283.4
23:31:39.069 INFO ProgressMeter - chr6:135212997 47.4 13390 282.2
23:31:52.160 INFO ProgressMeter - chr6:135216713 47.7 13420 281.6
23:32:03.863 INFO ProgressMeter - chr6:149683606 47.9 13470 281.5
23:32:13.879 INFO ProgressMeter - chr6:151880653 48.0 13510 281.3
23:32:25.402 INFO ProgressMeter - chr6:157084750 48.2 13560 281.2
23:32:36.614 INFO ProgressMeter - chr6:161049344 48.4 13610 281.2
23:32:47.018 INFO ProgressMeter - chr6:163565944 48.6 13680 281.6
23:32:58.041 INFO ProgressMeter - chr7:6391922 48.8 13740 281.8
23:33:09.834 INFO ProgressMeter - chr7:13907628 49.0 13780 281.5
23:33:20.598 INFO ProgressMeter - chr7:13932518 49.1 13800 280.8
23:33:31.028 INFO ProgressMeter - chr7:13937333 49.3 13830 280.5
23:33:49.277 INFO ProgressMeter - chr7:13942473 49.6 13860 279.3
23:34:02.875 INFO ProgressMeter - chr7:13947642 49.8 13890 278.7
23:34:13.479 INFO ProgressMeter - chr7:13950861 50.0 13910 278.1
23:34:27.846 INFO ProgressMeter - chr7:13955090 50.3 13940 277.4
23:34:38.899 INFO ProgressMeter - chr7:13960226 50.4 13970 277.0
23:34:52.665 INFO ProgressMeter - chr7:13966403 50.7 14000 276.3
23:35:05.198 INFO ProgressMeter - chr7:13971897 50.9 14040 275.9
23:35:22.651 INFO ProgressMeter - chr7:13976346 51.2 14070 275.0
23:35:35.781 INFO ProgressMeter - chr7:13981662 51.4 14110 274.6
23:35:48.272 INFO ProgressMeter - chr7:13985887 51.6 14140 274.0
23:36:00.160 INFO ProgressMeter - chr7:41690520 51.8 14170 273.6
23:36:10.266 INFO ProgressMeter - chr7:55153717 52.0 14210 273.5
23:36:24.266 INFO ProgressMeter - chr7:55169044 52.2 14250 273.0
23:36:34.947 INFO ProgressMeter - chr7:55176993 52.4 14280 272.6
23:36:45.725 INFO ProgressMeter - chr7:55183609 52.6 14310 272.3
23:36:56.880 INFO ProgressMeter - chr7:78185627 52.7 14360 272.3
23:37:08.568 INFO ProgressMeter - chr7:86839631 52.9 14420 272.4
23:37:18.706 INFO ProgressMeter - chr7:102198781 53.1 14480 272.7
23:37:29.196 INFO ProgressMeter - chr7:106872872 53.3 14530 272.7
23:37:40.498 INFO ProgressMeter - chr7:116773120 53.5 14580 272.7
23:37:51.301 INFO ProgressMeter - chr7:140753273 53.6 14630 272.7
23:38:01.992 INFO ProgressMeter - chr7:140805691 53.8 14680 272.7
23:38:12.630 INFO ProgressMeter - chr7:148826551 54.0 14750 273.1
23:38:23.981 INFO ProgressMeter - chr7:152176489 54.2 14810 273.3
23:38:34.190 INFO ProgressMeter - chr7:152202932 54.4 14850 273.2
23:38:44.240 INFO ProgressMeter - chr8:23678488 54.5 14920 273.6
23:38:54.286 INFO ProgressMeter - chr8:32646793 54.7 14980 273.9
23:39:04.881 INFO ProgressMeter - chr8:37697548 54.9 15020 273.7
23:39:17.087 INFO ProgressMeter - chr8:38418226 55.1 15080 273.8
23:39:30.448 INFO ProgressMeter - chr8:41934582 55.3 15130 273.6
23:39:40.511 INFO ProgressMeter - chr8:47788989 55.5 15180 273.7
23:39:51.577 INFO ProgressMeter - chr8:47893323 55.7 15240 273.8
23:40:02.423 INFO ProgressMeter - chr8:68038157 55.8 15310 274.2
23:40:13.001 INFO ProgressMeter - chr8:89970362 56.0 15370 274.4
23:40:23.070 INFO ProgressMeter - chr8:127731668 56.2 15420 274.5
23:40:34.137 INFO ProgressMeter - chr8:144511429 56.4 15470 274.5
23:40:44.396 INFO ProgressMeter - chr9:5089726 56.5 15540 274.9
23:40:55.667 INFO ProgressMeter - chr9:20354806 56.7 15620 275.4
23:41:05.916 INFO ProgressMeter - chr9:35078603 56.9 15680 275.6
23:41:19.575 INFO ProgressMeter - chr9:84743231 57.1 15750 275.7
23:41:30.969 INFO ProgressMeter - chr9:84814133 57.3 15790 275.5
23:41:43.936 INFO ProgressMeter - chr9:84864381 57.5 15820 275.0
23:41:57.188 INFO ProgressMeter - chr9:84873897 57.7 15850 274.5
23:42:07.513 INFO ProgressMeter - chr9:85021658 57.9 15880 274.2
23:42:20.097 INFO ProgressMeter - chr9:85026786 58.1 15910 273.7
23:42:30.754 INFO ProgressMeter - chr9:95478998 58.3 15970 273.9
23:42:41.936 INFO ProgressMeter - chr9:130835253 58.5 16040 274.2
23:42:53.759 INFO ProgressMeter - chr9:132897182 58.7 16090 274.2
23:43:05.203 INFO ProgressMeter - chr9:136507953 58.9 16150 274.3
23:43:15.438 INFO ProgressMeter - chrX:15818585 59.1 16230 274.8
23:43:26.011 INFO ProgressMeter - chrX:45051707 59.2 16290 275.0
23:43:36.062 INFO ProgressMeter - chrX:47186063 59.4 16350 275.3
23:43:48.941 INFO ProgressMeter - chrX:49035180 59.6 16410 275.3
23:43:59.167 INFO ProgressMeter - chrX:49040453 59.8 16440 275.0
23:44:10.380 INFO ProgressMeter - chrX:53224738 60.0 16490 275.0
23:44:22.148 INFO ProgressMeter - chrX:64190179 60.2 16540 274.9
23:44:35.317 INFO ProgressMeter - chrX:67545196 60.4 16570 274.4
23:44:46.757 INFO ProgressMeter - chrX:71121637 60.6 16630 274.5
23:45:00.819 INFO ProgressMeter - chrX:71375165 60.8 16690 274.5
23:45:10.823 INFO ProgressMeter - chrX:77557522 61.0 16740 274.5
23:45:21.254 INFO ProgressMeter - chrX:77684937 61.1 16790 274.6
23:45:31.570 INFO ProgressMeter - chrX:124051119 61.3 16860 275.0
23:45:42.299 INFO ProgressMeter - chrX:130020983 61.5 16910 275.0
23:45:48.067 INFO Mutect2 - 683158 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
3 read(s) filtered by: ReadLengthReadFilter
174 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
683335 total reads filtered out of 125570501 reads processed
23:45:48.067 INFO ProgressMeter - chrY:19742699 61.6 16977 275.6
23:45:48.067 INFO ProgressMeter - Traversal complete. Processed 16977 total regions in 61.6 minutes.
23:45:48.084 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.3716379430000005
23:45:48.084 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 362.500226976
23:45:48.085 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.62 sec
23:45:48.085 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:45:48 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 61.61 minutes.
Runtime.totalMemory()=4664066048
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 LS0888_tumor.bam --tumor-sample LS0888 -L TST500C_manifest.bed -O LS0888.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:45:49.722 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
23:45:49.821 INFO FilterMutectCalls - ------------------------------------------------------------
23:45:49.824 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:45:49.824 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:45:49.824 INFO FilterMutectCalls - Executing as ?@nf-6e27ec033b0f87e3a9b18dda38d3a6e3-02ca2-qlsvz on Linux v6.12.88 amd64
23:45:49.824 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:45:49.824 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:45:49 PM GMT
23:45:49.824 INFO FilterMutectCalls - ------------------------------------------------------------
23:45:49.824 INFO FilterMutectCalls - ------------------------------------------------------------
23:45:49.825 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:45:49.825 INFO FilterMutectCalls - Picard Version: 3.1.1
23:45:49.825 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:45:49.825 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:45:49.825 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:45:49.825 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:45:49.825 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:45:49.825 INFO FilterMutectCalls - Deflater: IntelDeflater
23:45:49.829 INFO FilterMutectCalls - Inflater: IntelInflater
23:45:49.829 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:45:49.829 INFO FilterMutectCalls - Requester pays: disabled
23:45:49.829 INFO FilterMutectCalls - Initializing engine
23:45:49.981 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.SOlxRmCbkf/LS0888.mutect2.raw.vcf.gz
23:45:50.089 INFO FilterMutectCalls - Done initializing engine
23:45:50.143 INFO ProgressMeter - Starting traversal
23:45:50.144 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:45:50.145 INFO FilterMutectCalls - Starting pass 0 through the variants
23:45:51.550 INFO FilterMutectCalls - Finished pass 0 through the variants
23:45:56.861 INFO FilterMutectCalls - Starting pass 1 through the variants
23:45:58.481 INFO FilterMutectCalls - Finished pass 1 through the variants
23:45:59.458 INFO FilterMutectCalls - Starting pass 2 through the variants
23:46:00.575 INFO ProgressMeter - chr6:29945075 0.2 7000 40276.2
23:46:01.047 INFO FilterMutectCalls - Finished pass 2 through the variants
23:46:01.048 INFO FilterMutectCalls - Starting pass 3 through the variants
23:46:02.399 INFO FilterMutectCalls - Finished pass 3 through the variants
23:46:02.405 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:46:02.406 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:46:02.406 INFO ProgressMeter - chr7:13986102 0.2 10340 50595.3
23:46:02.406 INFO ProgressMeter - Traversal complete. Processed 10340 total variants in 0.2 minutes.
23:46:02.416 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:46:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=343932928
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 LS0888.mutect2.raw.vcf.gz --stats LS0888.mutect2.raw.vcf.gz.stats -O LS0888.mutect2.filtered.vcf.gz
23:46:03.583 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
23:46:03.678 INFO SelectVariants - ------------------------------------------------------------
23:46:03.680 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:46:03.680 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:46:03.680 INFO SelectVariants - Executing as ?@nf-6e27ec033b0f87e3a9b18dda38d3a6e3-02ca2-qlsvz on Linux v6.12.88 amd64
23:46:03.680 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:46:03.681 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:46:03 PM GMT
23:46:03.681 INFO SelectVariants - ------------------------------------------------------------
23:46:03.681 INFO SelectVariants - ------------------------------------------------------------
23:46:03.681 INFO SelectVariants - HTSJDK Version: 4.1.0
23:46:03.682 INFO SelectVariants - Picard Version: 3.1.1
23:46:03.682 INFO SelectVariants - Built for Spark Version: 3.5.0
23:46:03.682 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:46:03.682 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:46:03.682 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:46:03.682 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:46:03.682 INFO SelectVariants - Deflater: IntelDeflater
23:46:03.682 INFO SelectVariants - Inflater: IntelInflater
23:46:03.682 INFO SelectVariants - GCS max retries/reopens: 20
23:46:03.682 INFO SelectVariants - Requester pays: disabled
23:46:03.683 INFO SelectVariants - Initializing engine
23:46:03.804 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.SOlxRmCbkf/LS0888.mutect2.filtered.vcf.gz
23:46:03.908 INFO SelectVariants - Done initializing engine
23:46:03.946 INFO ProgressMeter - Starting traversal
23:46:03.947 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:46:04.023 INFO ProgressMeter - chr6:151804309 0.0 2585 2095945.9
23:46:04.023 INFO ProgressMeter - Traversal complete. Processed 2585 total variants in 0.0 minutes.
23:46:04.033 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:46:04 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=503316480
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 LS0888.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0888.mutect2.pass.vcf.gz