Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0926/LS0926_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/e0/c8590237ba69d8d5b1afb4d6805fd5/.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/LS0926/LS0926_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/e0/c8590237ba69d8d5b1afb4d6805fd5/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:32.951 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
22:44:33.055 INFO Mutect2 - ------------------------------------------------------------
22:44:33.058 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:33.058 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:33.058 INFO Mutect2 - Executing as ?@nf-e0c8590237ba69d8d5b1afb4d6805fd5-217e5-l4k7g on Linux v6.12.88 amd64
22:44:33.058 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:33.058 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:32 PM GMT
22:44:33.058 INFO Mutect2 - ------------------------------------------------------------
22:44:33.058 INFO Mutect2 - ------------------------------------------------------------
22:44:33.059 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:33.059 INFO Mutect2 - Picard Version: 3.1.1
22:44:33.059 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:33.059 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:33.059 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:33.059 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:33.059 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:33.059 INFO Mutect2 - Deflater: IntelDeflater
22:44:33.059 INFO Mutect2 - Inflater: IntelInflater
22:44:33.060 INFO Mutect2 - GCS max retries/reopens: 20
22:44:33.060 INFO Mutect2 - Requester pays: disabled
22:44:33.060 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.QQZDoMkJUK/LS0926_tumor.bam.bai is older than BAM /tmp/nxf.QQZDoMkJUK/LS0926_tumor.bam
22:44:33.223 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.QQZDoMkJUK/af-only-gnomad.hg38.vcf.gz
22:44:33.335 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.QQZDoMkJUK/TST500C_manifest.bed
22:44:33.369 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:33.397 INFO Mutect2 - Done initializing engine
22:44:33.407 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
22:44:33.408 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
22:44:33.409 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:33.409 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:33.419 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
22:44:33.431 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:33.431 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:33.432 INFO IntelPairHmm - Available threads: 384
22:44:33.432 INFO IntelPairHmm - Requested threads: 4
22:44:33.432 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:33.481 INFO ProgressMeter - Starting traversal
22:44:33.482 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:44.894 INFO ProgressMeter - chr1:9721759 0.2 40 210.3
22:44:57.071 INFO ProgressMeter - chr1:11233396 0.4 110 279.8
22:45:07.574 INFO ProgressMeter - chr1:15930193 0.6 160 281.6
22:45:17.758 INFO ProgressMeter - chr1:15937379 0.7 190 257.5
22:45:30.187 INFO ProgressMeter - chr1:18747391 0.9 240 253.9
22:45:43.315 INFO ProgressMeter - chr1:26774927 1.2 290 249.2
22:45:53.470 INFO ProgressMeter - chr1:39891087 1.3 340 255.0
22:46:03.484 INFO ProgressMeter - chr1:39907006 1.5 390 260.0
22:46:13.503 INFO ProgressMeter - chr1:46248510 1.7 450 269.9
22:46:24.535 INFO ProgressMeter - chr1:64864785 1.9 510 275.5
22:46:35.138 INFO ProgressMeter - chr1:114714110 2.0 600 295.9
22:46:47.088 INFO ProgressMeter - chr1:119915924 2.2 650 291.9
22:46:57.105 INFO ProgressMeter - chr1:149840745 2.4 700 292.4
22:47:10.007 INFO ProgressMeter - chr1:156873321 2.6 740 283.7
22:47:20.941 INFO ProgressMeter - chr1:158614264 2.8 770 275.9
22:47:31.272 INFO ProgressMeter - chr1:158677770 3.0 830 280.1
22:47:41.575 INFO ProgressMeter - chr1:179108158 3.1 900 287.1
22:47:52.136 INFO ProgressMeter - chr1:204457035 3.3 970 293.0
22:48:02.221 INFO ProgressMeter - chr1:204544075 3.5 1020 293.2
22:48:13.240 INFO ProgressMeter - chr1:226365952 3.7 1090 297.6
22:48:24.773 INFO ProgressMeter - chr1:243501645 3.9 1150 298.3
22:48:36.462 INFO ProgressMeter - chr10:27006896 4.0 1200 296.3
22:48:47.858 INFO ProgressMeter - chr10:32009008 4.2 1260 297.2
22:48:58.436 INFO ProgressMeter - chr10:43106374 4.4 1320 298.9
22:49:08.544 INFO ProgressMeter - chr10:43115073 4.6 1350 294.5
22:49:21.363 INFO ProgressMeter - chr10:43126883 4.8 1390 289.7
22:49:31.611 INFO ProgressMeter - chr10:68645596 5.0 1430 287.8
22:49:42.715 INFO ProgressMeter - chr10:87952116 5.2 1500 291.0
22:49:53.305 INFO ProgressMeter - chr10:101775548 5.3 1550 290.8
22:50:05.690 INFO ProgressMeter - chr10:110602453 5.5 1610 290.8
22:50:18.561 INFO ProgressMeter - chr10:121482475 5.8 1660 288.6
22:50:30.031 INFO ProgressMeter - chr11:533837 5.9 1720 289.4
22:50:41.004 INFO ProgressMeter - chr11:61437623 6.1 1780 290.6
22:50:51.917 INFO ProgressMeter - chr11:67434580 6.3 1840 291.7
22:51:02.855 INFO ProgressMeter - chr11:69696837 6.5 1890 291.2
22:51:13.668 INFO ProgressMeter - chr11:69703259 6.7 1920 287.9
22:51:25.115 INFO ProgressMeter - chr11:69776847 6.9 1970 287.1
22:51:37.669 INFO ProgressMeter - chr11:69810832 7.1 1990 281.5
22:51:49.700 INFO ProgressMeter - chr11:69819063 7.3 2020 277.8
22:52:02.037 INFO ProgressMeter - chr11:77358899 7.5 2080 278.2
22:52:12.412 INFO ProgressMeter - chr11:94437175 7.6 2150 281.1
22:52:30.400 INFO ProgressMeter - chr11:102325464 7.9 2210 278.0
22:52:40.745 INFO ProgressMeter - chr11:112093174 8.1 2290 282.0
22:52:50.922 INFO ProgressMeter - chr11:118493055 8.3 2330 281.0
22:53:01.651 INFO ProgressMeter - chr11:119232446 8.5 2370 279.8
22:53:12.739 INFO ProgressMeter - chr11:125637165 8.7 2410 278.5
22:53:29.134 INFO ProgressMeter - chr11:128460486 8.9 2450 274.4
22:53:39.854 INFO ProgressMeter - chr11:128768116 9.1 2480 272.3
22:53:51.336 INFO ProgressMeter - chr12:323598 9.3 2530 272.1
22:54:02.950 INFO ProgressMeter - chr12:4379370 9.5 2600 273.9
22:54:13.199 INFO ProgressMeter - chr12:4444868 9.7 2650 274.3
22:54:29.305 INFO ProgressMeter - chr12:6602099 9.9 2710 272.9
22:54:42.271 INFO ProgressMeter - chr12:11856132 10.1 2740 270.0
22:54:55.298 INFO ProgressMeter - chr12:11860716 10.4 2780 268.2
22:55:07.419 INFO ProgressMeter - chr12:11865378 10.6 2810 266.0
22:55:19.798 INFO ProgressMeter - chr12:11884570 10.8 2840 263.6
22:55:30.599 INFO ProgressMeter - chr12:25227232 11.0 2920 266.6
22:55:43.663 INFO ProgressMeter - chr12:45852220 11.2 2970 265.9
22:55:54.846 INFO ProgressMeter - chr12:49032549 11.4 3020 265.9
22:56:04.930 INFO ProgressMeter - chr12:49037635 11.5 3040 263.8
22:56:16.789 INFO ProgressMeter - chr12:49050884 11.7 3090 263.6
22:56:28.580 INFO ProgressMeter - chr12:56080633 11.9 3140 263.5
22:56:39.521 INFO ProgressMeter - chr12:57089317 12.1 3200 264.4
22:56:49.643 INFO ProgressMeter - chr12:57464671 12.3 3230 263.3
22:57:01.903 INFO ProgressMeter - chr12:57751868 12.5 3280 263.0
22:57:12.909 INFO ProgressMeter - chr12:68844245 12.7 3340 263.9
22:57:23.543 INFO ProgressMeter - chr12:114671895 12.8 3400 264.9
22:57:33.974 INFO ProgressMeter - chr12:132625643 13.0 3450 265.2
22:57:44.446 INFO ProgressMeter - chr12:132677361 13.2 3500 265.5
22:57:56.908 INFO ProgressMeter - chr13:21678821 13.4 3540 264.4
22:58:07.269 INFO ProgressMeter - chr13:28050195 13.6 3620 266.9
22:58:19.371 INFO ProgressMeter - chr13:28387867 13.8 3670 266.6
22:58:30.647 INFO ProgressMeter - chr13:32336263 14.0 3720 266.6
22:58:41.579 INFO ProgressMeter - chr13:32380005 14.1 3770 266.7
22:58:52.623 INFO ProgressMeter - chr13:72780844 14.3 3850 268.9
22:59:04.024 INFO ProgressMeter - chr13:102872305 14.5 3920 270.2
22:59:14.576 INFO ProgressMeter - chr13:113304211 14.7 3970 270.3
22:59:25.725 INFO ProgressMeter - chr14:23183020 14.9 4010 269.7
22:59:37.163 INFO ProgressMeter - chr14:37591663 15.1 4070 270.2
22:59:48.143 INFO ProgressMeter - chr14:65076474 15.2 4120 270.3
22:59:58.792 INFO ProgressMeter - chr14:95095770 15.4 4170 270.4
23:00:09.770 INFO ProgressMeter - chr14:104302924 15.6 4230 271.1
23:00:22.355 INFO ProgressMeter - chr15:34350702 15.8 4280 270.6
23:00:32.480 INFO ProgressMeter - chr15:40731053 16.0 4310 269.7
23:00:42.673 INFO ProgressMeter - chr15:41754435 16.2 4350 269.3
23:00:53.123 INFO ProgressMeter - chr15:66436862 16.3 4420 270.7
23:01:03.200 INFO ProgressMeter - chr15:87978120 16.5 4470 271.0
23:01:13.246 INFO ProgressMeter - chr15:89299798 16.7 4530 271.9
23:01:23.810 INFO ProgressMeter - chr15:90809135 16.8 4590 272.6
23:01:35.142 INFO ProgressMeter - chr15:98896755 17.0 4650 273.1
23:01:45.688 INFO ProgressMeter - chr16:2054294 17.2 4700 273.2
23:01:56.143 INFO ProgressMeter - chr16:2171570 17.4 4760 273.9
23:02:07.072 INFO ProgressMeter - chr16:3595603 17.6 4830 275.1
23:02:17.923 INFO ProgressMeter - chr16:3736648 17.7 4860 273.9
23:02:28.686 INFO ProgressMeter - chr16:9822262 17.9 4910 274.0
23:02:39.533 INFO ProgressMeter - chr16:23626292 18.1 4970 274.6
23:02:50.408 INFO ProgressMeter - chr16:56798474 18.3 5030 275.1
23:03:01.400 INFO ProgressMeter - chr16:68819381 18.5 5090 275.7
23:03:13.187 INFO ProgressMeter - chr16:72795216 18.7 5120 274.4
23:03:27.446 INFO ProgressMeter - chr16:72957880 18.9 5150 272.5
23:03:38.028 INFO ProgressMeter - chr16:81937756 19.1 5200 272.6
23:03:49.482 INFO ProgressMeter - chr16:89283301 19.3 5240 272.0
23:04:00.367 INFO ProgressMeter - chr16:89778941 19.4 5300 272.5
23:04:16.119 INFO ProgressMeter - chr17:7676192 19.7 5370 272.4
23:04:27.498 INFO ProgressMeter - chr17:16057512 19.9 5440 273.4
23:04:39.097 INFO ProgressMeter - chr17:17224086 20.1 5510 274.2
23:04:50.165 INFO ProgressMeter - chr17:31337581 20.3 5580 275.2
23:05:02.850 INFO ProgressMeter - chr17:39490555 20.5 5650 275.8
23:05:13.944 INFO ProgressMeter - chr17:39712320 20.7 5700 275.7
23:05:24.356 INFO ProgressMeter - chr17:40396371 20.8 5750 275.8
23:05:34.945 INFO ProgressMeter - chr17:42305608 21.0 5820 276.8
23:05:45.059 INFO ProgressMeter - chr17:43090706 21.2 5890 277.9
23:05:58.661 INFO ProgressMeter - chr17:43531009 21.4 5940 277.3
23:06:09.449 INFO ProgressMeter - chr17:43537685 21.6 5980 276.9
23:06:25.904 INFO ProgressMeter - chr17:43544045 21.9 6020 275.2
23:06:36.603 INFO ProgressMeter - chr17:48725137 22.1 6060 274.8
23:06:48.277 INFO ProgressMeter - chr17:59896882 22.2 6120 275.1
23:06:58.975 INFO ProgressMeter - chr17:60600713 22.4 6170 275.1
23:07:11.075 INFO ProgressMeter - chr17:65537531 22.6 6230 275.3
23:07:21.204 INFO ProgressMeter - chr17:76736797 22.8 6280 275.5
23:07:32.829 INFO ProgressMeter - chr18:22171443 23.0 6350 276.2
23:07:44.679 INFO ProgressMeter - chr18:44952307 23.2 6410 276.5
23:07:54.774 INFO ProgressMeter - chr18:58747403 23.4 6470 277.0
23:08:05.545 INFO ProgressMeter - chr19:1631947 23.5 6520 277.0
23:08:15.811 INFO ProgressMeter - chr19:3118922 23.7 6580 277.6
23:08:26.675 INFO ProgressMeter - chr19:5218785 23.9 6640 278.0
23:08:37.112 INFO ProgressMeter - chr19:7167966 24.1 6700 278.5
23:08:47.910 INFO ProgressMeter - chr19:10175538 24.2 6750 278.5
23:08:57.970 INFO ProgressMeter - chr19:11012947 24.4 6800 278.6
23:09:08.732 INFO ProgressMeter - chr19:14517219 24.6 6850 278.6
23:09:20.746 INFO ProgressMeter - chr19:15181574 24.8 6900 278.4
23:09:33.014 INFO ProgressMeter - chr19:15253557 25.0 6950 278.1
23:09:46.909 INFO ProgressMeter - chr19:17844232 25.2 7000 277.5
23:09:59.888 INFO ProgressMeter - chr19:29819173 25.4 7060 277.5
23:10:12.064 INFO ProgressMeter - chr19:35723732 25.6 7120 277.7
23:10:22.372 INFO ProgressMeter - chr19:40235261 25.8 7170 277.7
23:10:33.708 INFO ProgressMeter - chr19:41226753 26.0 7220 277.7
23:10:45.129 INFO ProgressMeter - chr19:41877303 26.2 7250 276.8
23:10:56.792 INFO ProgressMeter - chr19:45349990 26.4 7300 276.6
23:11:07.223 INFO ProgressMeter - chr19:45406232 26.6 7360 277.1
23:11:18.941 INFO ProgressMeter - chr19:50402203 26.8 7420 277.3
23:11:33.062 INFO ProgressMeter - chr2:15940859 27.0 7480 277.1
23:11:44.497 INFO ProgressMeter - chr2:17781519 27.2 7530 277.0
23:11:55.271 INFO ProgressMeter - chr2:25743527 27.4 7580 277.0
23:12:06.161 INFO ProgressMeter - chr2:29222487 27.5 7630 277.0
23:12:20.024 INFO ProgressMeter - chr2:29227572 27.8 7660 275.8
23:12:30.604 INFO ProgressMeter - chr2:42288225 28.0 7710 275.8
23:12:43.792 INFO ProgressMeter - chr2:47463029 28.2 7760 275.5
23:12:54.512 INFO ProgressMeter - chr2:58165722 28.4 7810 275.5
23:13:07.264 INFO ProgressMeter - chr2:96262363 28.6 7870 275.5
23:13:19.107 INFO ProgressMeter - chr2:108765335 28.8 7940 276.1
23:13:31.354 INFO ProgressMeter - chr2:111127473 29.0 7980 275.5
23:13:42.787 INFO ProgressMeter - chr2:113223984 29.2 8020 275.1
23:13:55.107 INFO ProgressMeter - chr2:113227553 29.4 8050 274.2
23:14:13.990 INFO ProgressMeter - chr2:113233757 29.7 8090 272.6
23:14:24.333 INFO ProgressMeter - chr2:136115073 29.8 8140 272.7
23:14:35.448 INFO ProgressMeter - chr2:140776096 30.0 8220 273.7
23:14:46.077 INFO ProgressMeter - chr2:172556210 30.2 8280 274.1
23:14:57.326 INFO ProgressMeter - chr2:197401398 30.4 8360 275.0
23:15:07.561 INFO ProgressMeter - chr2:211383831 30.6 8420 275.5
23:15:21.238 INFO ProgressMeter - chr2:222201363 30.8 8490 275.7
23:15:32.902 INFO ProgressMeter - chr2:222208403 31.0 8530 275.2
23:15:46.122 INFO ProgressMeter - chr2:222215811 31.2 8570 274.6
23:15:57.083 INFO ProgressMeter - chr2:222293628 31.4 8600 273.9
23:16:08.140 INFO ProgressMeter - chr2:226796732 31.6 8650 273.9
23:16:18.202 INFO ProgressMeter - chr20:31721953 31.7 8700 274.1
23:16:29.337 INFO ProgressMeter - chr20:32800151 31.9 8750 274.0
23:16:41.397 INFO ProgressMeter - chr20:42677998 32.1 8830 274.8
23:16:52.856 INFO ProgressMeter - chr20:53581459 32.3 8880 274.7
23:17:03.688 INFO ProgressMeter - chr20:58898939 32.5 8930 274.7
23:17:15.342 INFO ProgressMeter - chr21:38381046 32.7 8990 274.9
23:17:27.848 INFO ProgressMeter - chr21:41465570 32.9 9040 274.7
23:17:38.896 INFO ProgressMeter - chr21:41490386 33.1 9070 274.1
23:17:50.803 INFO ProgressMeter - chr21:41493158 33.3 9090 273.1
23:18:05.641 INFO ProgressMeter - chr21:41503040 33.5 9130 272.2
23:18:17.502 INFO ProgressMeter - chr21:43094653 33.7 9170 271.8
23:18:28.008 INFO ProgressMeter - chr22:21807780 33.9 9230 272.2
23:18:42.586 INFO ProgressMeter - chr22:23291083 34.2 9270 271.4
23:18:52.767 INFO ProgressMeter - chr22:28707017 34.3 9330 271.8
23:19:06.517 INFO ProgressMeter - chr22:29285716 34.6 9400 272.1
23:19:17.810 INFO ProgressMeter - chr22:29683018 34.7 9450 272.0
23:19:30.225 INFO ProgressMeter - chr22:41178078 34.9 9510 272.1
23:19:40.620 INFO ProgressMeter - chr3:10142127 35.1 9570 272.5
23:19:53.194 INFO ProgressMeter - chr3:12357236 35.3 9610 272.0
23:20:05.018 INFO ProgressMeter - chr3:12362923 35.5 9640 271.4
23:20:15.938 INFO ProgressMeter - chr3:12370222 35.7 9680 271.1
23:20:27.499 INFO ProgressMeter - chr3:12377746 35.9 9720 270.7
23:20:40.102 INFO ProgressMeter - chr3:12649648 36.1 9780 270.8
23:20:51.291 INFO ProgressMeter - chr3:41233811 36.3 9850 271.4
23:21:04.021 INFO ProgressMeter - chr3:47123861 36.5 9910 271.4
23:21:14.667 INFO ProgressMeter - chr3:49897518 36.7 9970 271.8
23:21:26.380 INFO ProgressMeter - chr3:52627271 36.9 10030 272.0
23:21:36.652 INFO ProgressMeter - chr3:72817228 37.1 10100 272.6
23:21:46.852 INFO ProgressMeter - chr3:134951720 37.2 10160 273.0
23:21:58.063 INFO ProgressMeter - chr3:138663904 37.4 10230 273.5
23:22:09.154 INFO ProgressMeter - chr3:142522726 37.6 10310 274.2
23:22:20.521 INFO ProgressMeter - chr3:179218208 37.8 10390 275.0
23:22:31.055 INFO ProgressMeter - chr3:185449898 38.0 10450 275.3
23:22:42.118 INFO ProgressMeter - chr3:186787801 38.1 10500 275.3
23:22:53.305 INFO ProgressMeter - chr3:196058764 38.3 10560 275.5
23:23:04.283 INFO ProgressMeter - chr4:1806130 38.5 10630 276.0
23:23:15.798 INFO ProgressMeter - chr4:41746166 38.7 10700 276.4
23:23:27.156 INFO ProgressMeter - chr4:54695603 38.9 10760 276.6
23:23:38.695 INFO ProgressMeter - chr4:55079939 39.1 10800 276.3
23:23:50.600 INFO ProgressMeter - chr4:80271311 39.3 10870 276.7
23:24:04.097 INFO ProgressMeter - chr4:105236680 39.5 10950 277.1
23:24:16.285 INFO ProgressMeter - chr4:122826774 39.7 11000 277.0
23:24:26.658 INFO ProgressMeter - chr4:152352768 39.9 11080 277.8
23:24:36.680 INFO ProgressMeter - chr4:186603904 40.1 11130 277.9
23:24:47.500 INFO ProgressMeter - chr4:186636702 40.2 11170 277.6
23:24:59.402 INFO ProgressMeter - chr5:1294991 40.4 11220 277.5
23:25:09.802 INFO ProgressMeter - chr5:44328690 40.6 11310 278.5
23:25:20.313 INFO ProgressMeter - chr5:56884662 40.8 11370 278.8
23:25:31.350 INFO ProgressMeter - chr5:80761544 41.0 11440 279.3
23:25:44.412 INFO ProgressMeter - chr5:112840251 41.2 11530 280.0
23:25:54.975 INFO ProgressMeter - chr5:132587922 41.4 11580 280.0
23:26:05.515 INFO ProgressMeter - chr5:142630778 41.5 11640 280.3
23:26:16.130 INFO ProgressMeter - chr5:150056024 41.7 11690 280.3
23:26:28.079 INFO ProgressMeter - chr5:150135553 41.9 11750 280.4
23:26:38.904 INFO ProgressMeter - chr5:161701496 42.1 11800 280.3
23:26:49.463 INFO ProgressMeter - chr5:177091683 42.3 11840 280.1
23:27:00.008 INFO ProgressMeter - chr5:177210229 42.4 11880 279.9
23:27:11.236 INFO ProgressMeter - chr5:177515165 42.6 11930 279.9
23:27:22.439 INFO ProgressMeter - chr6:401769 42.8 11990 280.0
23:27:33.523 INFO ProgressMeter - chr6:20487934 43.0 12060 280.5
23:27:50.450 INFO ProgressMeter - chr6:29943266 43.3 12120 280.0
23:28:01.438 INFO ProgressMeter - chr6:30707676 43.5 12150 279.5
23:28:13.283 INFO ProgressMeter - chr6:32213686 43.7 12200 279.4
23:28:24.901 INFO ProgressMeter - chr6:35459329 43.9 12250 279.3
23:28:35.847 INFO ProgressMeter - chr6:42045281 44.0 12320 279.7
23:28:46.886 INFO ProgressMeter - chr6:106099298 44.2 12390 280.2
23:28:59.455 INFO ProgressMeter - chr6:117320260 44.4 12450 280.2
23:29:09.880 INFO ProgressMeter - chr6:117327035 44.6 12480 279.8
23:29:20.529 INFO ProgressMeter - chr6:117335697 44.8 12530 279.8
23:29:32.171 INFO ProgressMeter - chr6:117393222 45.0 12580 279.7
23:29:42.552 INFO ProgressMeter - chr6:135206107 45.2 12630 279.7
23:29:59.524 INFO ProgressMeter - chr6:135212044 45.4 12670 278.9
23:30:09.709 INFO ProgressMeter - chr6:135217080 45.6 12700 278.5
23:30:21.599 INFO ProgressMeter - chr6:149684011 45.8 12750 278.4
23:30:32.898 INFO ProgressMeter - chr6:152090622 46.0 12810 278.5
23:30:47.625 INFO ProgressMeter - chr6:156871612 46.2 12830 277.5
23:30:59.735 INFO ProgressMeter - chr6:161073464 46.4 12880 277.4
23:31:10.129 INFO ProgressMeter - chr7:2919370 46.6 12950 277.8
23:31:22.388 INFO ProgressMeter - chr7:13894120 46.8 13020 278.1
23:31:35.593 INFO ProgressMeter - chr7:13932708 47.0 13060 277.7
23:31:45.710 INFO ProgressMeter - chr7:13939554 47.2 13100 277.5
23:31:58.548 INFO ProgressMeter - chr7:13947455 47.4 13150 277.3
23:32:10.269 INFO ProgressMeter - chr7:13952907 47.6 13180 276.8
23:32:20.742 INFO ProgressMeter - chr7:13959722 47.8 13220 276.6
23:32:32.297 INFO ProgressMeter - chr7:13965411 48.0 13250 276.2
23:32:43.663 INFO ProgressMeter - chr7:13973666 48.2 13300 276.1
23:32:55.650 INFO ProgressMeter - chr7:13978457 48.4 13330 275.6
23:33:10.024 INFO ProgressMeter - chr7:13984064 48.6 13370 275.1
23:33:21.066 INFO ProgressMeter - chr7:13988302 48.8 13390 274.4
23:33:32.498 INFO ProgressMeter - chr7:50400516 49.0 13430 274.2
23:33:46.917 INFO ProgressMeter - chr7:55166527 49.2 13480 273.9
23:33:57.148 INFO ProgressMeter - chr7:55169975 49.4 13500 273.3
23:34:08.562 INFO ProgressMeter - chr7:55178498 49.6 13540 273.1
23:34:21.540 INFO ProgressMeter - chr7:55201323 49.8 13580 272.7
23:34:33.442 INFO ProgressMeter - chr7:86786750 50.0 13650 273.0
23:34:45.817 INFO ProgressMeter - chr7:102201339 50.2 13720 273.3
23:34:57.178 INFO ProgressMeter - chr7:106872711 50.4 13770 273.2
23:35:07.333 INFO ProgressMeter - chr7:116772032 50.6 13810 273.1
23:35:18.434 INFO ProgressMeter - chr7:140739810 50.7 13850 272.9
23:35:29.151 INFO ProgressMeter - chr7:140793630 50.9 13900 272.9
23:35:39.758 INFO ProgressMeter - chr7:142961793 51.1 13970 273.4
23:35:50.817 INFO ProgressMeter - chr7:152163006 51.3 14030 273.5
23:36:00.817 INFO ProgressMeter - chr7:152194438 51.5 14070 273.4
23:36:11.381 INFO ProgressMeter - chr8:11758291 51.6 14140 273.9
23:36:23.685 INFO ProgressMeter - chr8:32634151 51.8 14210 274.1
23:36:35.382 INFO ProgressMeter - chr8:37829259 52.0 14260 274.1
23:36:46.496 INFO ProgressMeter - chr8:38428344 52.2 14310 274.0
23:36:56.496 INFO ProgressMeter - chr8:41933155 52.4 14340 273.7
23:37:07.215 INFO ProgressMeter - chr8:47807135 52.6 14390 273.8
23:37:17.775 INFO ProgressMeter - chr8:47953618 52.7 14470 274.4
23:37:28.366 INFO ProgressMeter - chr8:68108224 52.9 14540 274.8
23:37:38.780 INFO ProgressMeter - chr8:116856164 53.1 14620 275.4
23:37:49.555 INFO ProgressMeter - chr8:127737355 53.3 14650 275.0
23:38:01.781 INFO ProgressMeter - chr8:127743489 53.5 14690 274.7
23:38:12.556 INFO ProgressMeter - chr9:5029781 53.7 14750 274.9
23:38:23.388 INFO ProgressMeter - chr9:8497240 53.8 14830 275.5
23:38:33.751 INFO ProgressMeter - chr9:21968227 54.0 14870 275.3
23:38:45.220 INFO ProgressMeter - chr9:83970716 54.2 14930 275.5
23:38:55.647 INFO ProgressMeter - chr9:84742675 54.4 14970 275.3
23:39:09.042 INFO ProgressMeter - chr9:84815205 54.6 15010 274.9
23:39:24.122 INFO ProgressMeter - chr9:84865606 54.8 15040 274.2
23:39:35.951 INFO ProgressMeter - chr9:84877541 55.0 15080 274.0
23:39:51.498 INFO ProgressMeter - chr9:90844065 55.3 15120 273.4
23:40:02.443 INFO ProgressMeter - chr9:95477643 55.5 15180 273.6
23:40:14.024 INFO ProgressMeter - chr9:126205716 55.7 15240 273.7
23:40:24.549 INFO ProgressMeter - chr9:132896656 55.9 15280 273.6
23:40:35.803 INFO ProgressMeter - chr9:136503296 56.0 15330 273.6
23:40:46.909 INFO ProgressMeter - chr9:136670948 56.2 15380 273.5
23:40:57.161 INFO ProgressMeter - chrX:45034929 56.4 15460 274.1
23:41:07.491 INFO ProgressMeter - chrX:48793995 56.6 15540 274.7
23:41:18.162 INFO ProgressMeter - chrX:49043109 56.7 15600 274.9
23:41:28.618 INFO ProgressMeter - chrX:53413146 56.9 15670 275.3
23:41:39.284 INFO ProgressMeter - chrX:67574654 57.1 15720 275.3
23:41:51.316 INFO ProgressMeter - chrX:71375165 57.3 15820 276.1
23:42:02.003 INFO ProgressMeter - chrX:111152408 57.5 15940 277.3
23:42:12.560 INFO ProgressMeter - chrX:134414995 57.7 16040 278.2
23:42:17.016 INFO Mutect2 - 892904 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
178 read(s) filtered by: ReadLengthReadFilter
112 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
893194 total reads filtered out of 124157389 reads processed
23:42:17.016 INFO ProgressMeter - chrY:20557826 57.7 16093 278.8
23:42:17.016 INFO ProgressMeter - Traversal complete. Processed 16093 total regions in 57.7 minutes.
23:42:17.032 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.496559201
23:42:17.032 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 362.24091727200005
23:42:17.032 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.24 sec
23:42:17.033 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:42:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 57.74 minutes.
Runtime.totalMemory()=4034920448
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 LS0926_tumor.bam --tumor-sample LS0926 -L TST500C_manifest.bed -O LS0926.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:42:18.308 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
23:42:18.410 INFO FilterMutectCalls - ------------------------------------------------------------
23:42:18.412 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:42:18.413 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:42:18.413 INFO FilterMutectCalls - Executing as ?@nf-e0c8590237ba69d8d5b1afb4d6805fd5-217e5-l4k7g on Linux v6.12.88 amd64
23:42:18.413 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:42:18.413 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:42:18 PM GMT
23:42:18.413 INFO FilterMutectCalls - ------------------------------------------------------------
23:42:18.413 INFO FilterMutectCalls - ------------------------------------------------------------
23:42:18.414 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:42:18.414 INFO FilterMutectCalls - Picard Version: 3.1.1
23:42:18.414 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:42:18.414 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:42:18.414 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:42:18.414 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:42:18.414 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:42:18.415 INFO FilterMutectCalls - Deflater: IntelDeflater
23:42:18.415 INFO FilterMutectCalls - Inflater: IntelInflater
23:42:18.415 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:42:18.415 INFO FilterMutectCalls - Requester pays: disabled
23:42:18.415 INFO FilterMutectCalls - Initializing engine
23:42:18.594 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.QQZDoMkJUK/LS0926.mutect2.raw.vcf.gz
23:42:18.706 INFO FilterMutectCalls - Done initializing engine
23:42:18.756 INFO ProgressMeter - Starting traversal
23:42:18.756 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:42:18.757 INFO FilterMutectCalls - Starting pass 0 through the variants
23:42:20.120 INFO FilterMutectCalls - Finished pass 0 through the variants
23:42:22.886 INFO FilterMutectCalls - Starting pass 1 through the variants
23:42:24.394 INFO FilterMutectCalls - Finished pass 1 through the variants
23:42:24.946 INFO FilterMutectCalls - Starting pass 2 through the variants
23:42:26.423 INFO FilterMutectCalls - Finished pass 2 through the variants
23:42:26.425 INFO FilterMutectCalls - Starting pass 3 through the variants
23:42:27.688 INFO FilterMutectCalls - Finished pass 3 through the variants
23:42:27.697 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:42:27.698 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:42:27.698 INFO ProgressMeter - chr7:154612851 0.1 11252 75508.3
23:42:27.698 INFO ProgressMeter - Traversal complete. Processed 11252 total variants in 0.1 minutes.
23:42:27.708 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:42:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=478150656
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 LS0926.mutect2.raw.vcf.gz --stats LS0926.mutect2.raw.vcf.gz.stats -O LS0926.mutect2.filtered.vcf.gz
23:42:29.005 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
23:42:29.126 INFO SelectVariants - ------------------------------------------------------------
23:42:29.129 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:42:29.129 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:42:29.129 INFO SelectVariants - Executing as ?@nf-e0c8590237ba69d8d5b1afb4d6805fd5-217e5-l4k7g on Linux v6.12.88 amd64
23:42:29.129 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:42:29.129 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:42:28 PM GMT
23:42:29.129 INFO SelectVariants - ------------------------------------------------------------
23:42:29.129 INFO SelectVariants - ------------------------------------------------------------
23:42:29.130 INFO SelectVariants - HTSJDK Version: 4.1.0
23:42:29.130 INFO SelectVariants - Picard Version: 3.1.1
23:42:29.130 INFO SelectVariants - Built for Spark Version: 3.5.0
23:42:29.130 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:42:29.130 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:42:29.130 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:42:29.130 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:42:29.131 INFO SelectVariants - Deflater: IntelDeflater
23:42:29.131 INFO SelectVariants - Inflater: IntelInflater
23:42:29.131 INFO SelectVariants - GCS max retries/reopens: 20
23:42:29.131 INFO SelectVariants - Requester pays: disabled
23:42:29.131 INFO SelectVariants - Initializing engine
23:42:29.290 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.QQZDoMkJUK/LS0926.mutect2.filtered.vcf.gz
23:42:29.399 INFO SelectVariants - Done initializing engine
23:42:29.433 INFO ProgressMeter - Starting traversal
23:42:29.433 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:42:29.512 INFO ProgressMeter - chr6:29944153 0.0 2813 2250400.0
23:42:29.512 INFO ProgressMeter - Traversal complete. Processed 2813 total variants in 0.0 minutes.
23:42:29.526 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:42:29 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0926.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0926.mutect2.pass.vcf.gz