Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0893/LS0893_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/0e/ec2f26c2c2964db6ffbccd08442747/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0893/LS0893_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/0e/ec2f26c2c2964db6ffbccd08442747/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:33.719 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
22:44:33.854 INFO Mutect2 - ------------------------------------------------------------
22:44:33.857 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:33.857 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:33.857 INFO Mutect2 - Executing as ?@nf-0eec2f26c2c2964db6ffbccd08442747-54705-hbpq2 on Linux v6.12.88 amd64
22:44:33.857 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:33.858 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:33 PM GMT
22:44:33.858 INFO Mutect2 - ------------------------------------------------------------
22:44:33.858 INFO Mutect2 - ------------------------------------------------------------
22:44:33.859 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:33.859 INFO Mutect2 - Picard Version: 3.1.1
22:44:33.859 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:33.859 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:33.859 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:33.860 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:33.860 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:33.860 INFO Mutect2 - Deflater: IntelDeflater
22:44:33.860 INFO Mutect2 - Inflater: IntelInflater
22:44:33.860 INFO Mutect2 - GCS max retries/reopens: 20
22:44:33.860 INFO Mutect2 - Requester pays: disabled
22:44:33.861 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.UVjpXjoRSs/LS0893_tumor.bam.bai is older than BAM /tmp/nxf.UVjpXjoRSs/LS0893_tumor.bam
22:44:34.007 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.UVjpXjoRSs/af-only-gnomad.hg38.vcf.gz
22:44:34.129 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.UVjpXjoRSs/TST500C_manifest.bed
22:44:34.163 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:34.191 INFO Mutect2 - Done initializing engine
22:44:34.201 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
22:44:34.202 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
22:44:34.203 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:34.203 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:34.212 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
22:44:34.220 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:34.220 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:34.220 INFO IntelPairHmm - Available threads: 384
22:44:34.221 INFO IntelPairHmm - Requested threads: 4
22:44:34.221 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:34.253 INFO ProgressMeter - Starting traversal
22:44:34.254 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:45.085 INFO ProgressMeter - chr1:9718848 0.2 50 277.0
22:44:56.539 INFO ProgressMeter - chr1:11199539 0.4 120 323.1
22:45:07.237 INFO ProgressMeter - chr1:15876655 0.5 170 309.3
22:45:17.969 INFO ProgressMeter - chr1:15932621 0.7 210 288.2
22:45:28.326 INFO ProgressMeter - chr1:17027747 0.9 250 277.4
22:45:41.457 INFO ProgressMeter - chr1:18747760 1.1 300 267.8
22:45:53.234 INFO ProgressMeter - chr1:26775016 1.3 360 273.5
22:46:04.242 INFO ProgressMeter - chr1:39891361 1.5 420 280.0
22:46:15.552 INFO ProgressMeter - chr1:43338097 1.7 480 284.3
22:46:26.269 INFO ProgressMeter - chr1:46080695 1.9 540 289.2
22:46:37.294 INFO ProgressMeter - chr1:64841521 2.1 610 297.5
22:46:48.563 INFO ProgressMeter - chr1:85270785 2.2 680 303.8
22:47:00.547 INFO ProgressMeter - chr1:117627382 2.4 750 307.6
22:47:12.413 INFO ProgressMeter - chr1:119935348 2.6 800 303.5
22:47:23.888 INFO ProgressMeter - chr1:156872721 2.8 870 307.7
22:47:38.377 INFO ProgressMeter - chr1:156879241 3.1 890 290.0
22:47:50.433 INFO ProgressMeter - chr1:158666314 3.3 960 293.6
22:48:01.174 INFO ProgressMeter - chr1:175988286 3.4 1030 298.7
22:48:11.415 INFO ProgressMeter - chr1:193122199 3.6 1090 301.2
22:48:22.164 INFO ProgressMeter - chr1:204469320 3.8 1160 305.4
22:48:33.023 INFO ProgressMeter - chr1:206476179 4.0 1220 306.6
22:48:43.186 INFO ProgressMeter - chr1:226392197 4.1 1290 310.9
22:48:55.906 INFO ProgressMeter - chr1:243502185 4.4 1350 309.6
22:49:07.731 INFO ProgressMeter - chr1:243563718 4.6 1380 302.8
22:49:18.824 INFO ProgressMeter - chr10:27048780 4.7 1440 303.6
22:49:29.941 INFO ProgressMeter - chr10:32022138 4.9 1500 304.4
22:49:40.136 INFO ProgressMeter - chr10:43112473 5.1 1550 304.0
22:49:50.665 INFO ProgressMeter - chr10:43117003 5.3 1590 301.5
22:50:01.435 INFO ProgressMeter - chr10:62091207 5.5 1640 300.8
22:50:12.174 INFO ProgressMeter - chr10:68645420 5.6 1680 298.3
22:50:22.204 INFO ProgressMeter - chr10:86921522 5.8 1730 298.3
22:50:35.944 INFO ProgressMeter - chr10:101770327 6.0 1810 300.3
22:50:46.722 INFO ProgressMeter - chr10:102627173 6.2 1880 302.8
22:50:57.397 INFO ProgressMeter - chr10:110602075 6.4 1920 300.7
22:51:11.092 INFO ProgressMeter - chr10:121481770 6.6 1980 299.4
22:51:22.433 INFO ProgressMeter - chr10:121544939 6.8 2030 298.4
22:51:33.574 INFO ProgressMeter - chr11:22625538 7.0 2090 299.1
22:51:44.753 INFO ProgressMeter - chr11:64809692 7.2 2160 301.0
22:51:56.565 INFO ProgressMeter - chr11:69653994 7.4 2230 302.5
22:52:06.638 INFO ProgressMeter - chr11:69702708 7.5 2270 301.1
22:52:20.097 INFO ProgressMeter - chr11:69778815 7.8 2340 301.4
22:52:32.811 INFO ProgressMeter - chr11:69814632 8.0 2370 297.1
22:52:44.219 INFO ProgressMeter - chr11:76544772 8.2 2430 297.6
22:52:54.770 INFO ProgressMeter - chr11:77388125 8.3 2480 297.3
22:53:05.391 INFO ProgressMeter - chr11:94447217 8.5 2540 298.2
22:53:24.244 INFO ProgressMeter - chr11:102324888 8.8 2600 294.3
22:53:34.830 INFO ProgressMeter - chr11:108297285 9.0 2660 295.2
22:53:45.376 INFO ProgressMeter - chr11:118472398 9.2 2720 296.1
22:53:55.734 INFO ProgressMeter - chr11:118502696 9.4 2770 296.0
22:54:07.277 INFO ProgressMeter - chr11:119274830 9.6 2820 295.3
22:54:19.160 INFO ProgressMeter - chr11:125637447 9.7 2860 293.4
22:54:29.585 INFO ProgressMeter - chr11:128459801 9.9 2900 292.3
22:54:40.317 INFO ProgressMeter - chr11:128484821 10.1 2920 289.1
22:54:51.152 INFO ProgressMeter - chr11:128812674 10.3 2970 288.9
22:55:02.275 INFO ProgressMeter - chr12:388925 10.5 3030 289.5
22:55:12.603 INFO ProgressMeter - chr12:4375229 10.6 3090 290.4
22:55:23.977 INFO ProgressMeter - chr12:4442023 10.8 3150 290.9
22:55:35.780 INFO ProgressMeter - chr12:6595332 11.0 3210 291.1
22:55:47.080 INFO ProgressMeter - chr12:11855349 11.2 3250 289.8
22:55:59.460 INFO ProgressMeter - chr12:11859905 11.4 3290 288.1
22:56:09.969 INFO ProgressMeter - chr12:11863287 11.6 3320 286.3
22:56:25.429 INFO ProgressMeter - chr12:11868686 11.9 3360 283.5
22:56:35.844 INFO ProgressMeter - chr12:18546321 12.0 3420 284.4
22:56:46.845 INFO ProgressMeter - chr12:25248153 12.2 3480 285.0
22:56:57.619 INFO ProgressMeter - chr12:45851666 12.4 3530 284.9
22:57:10.211 INFO ProgressMeter - chr12:49032233 12.6 3590 284.9
22:57:22.788 INFO ProgressMeter - chr12:49040329 12.8 3630 283.4
22:57:35.281 INFO ProgressMeter - chr12:49051476 13.0 3690 283.5
22:57:45.698 INFO ProgressMeter - chr12:51986848 13.2 3750 284.3
22:57:55.871 INFO ProgressMeter - chr12:56099646 13.4 3810 285.2
22:58:06.595 INFO ProgressMeter - chr12:57094420 13.5 3860 285.1
22:58:18.015 INFO ProgressMeter - chr12:57747226 13.7 3920 285.5
22:58:28.301 INFO ProgressMeter - chr12:68828769 13.9 3990 287.0
22:58:38.540 INFO ProgressMeter - chr12:92145386 14.1 4030 286.4
22:58:49.240 INFO ProgressMeter - chr12:114676351 14.2 4100 287.7
22:59:00.124 INFO ProgressMeter - chr12:132639180 14.4 4160 288.3
22:59:10.268 INFO ProgressMeter - chr13:20327527 14.6 4220 289.0
22:59:20.844 INFO ProgressMeter - chr13:21676365 14.8 4260 288.3
22:59:31.975 INFO ProgressMeter - chr13:28035933 15.0 4330 289.4
22:59:42.301 INFO ProgressMeter - chr13:28386232 15.1 4380 289.4
22:59:54.036 INFO ProgressMeter - chr13:28389528 15.3 4410 287.7
23:00:05.739 INFO ProgressMeter - chr13:32337122 15.5 4470 287.9
23:00:17.382 INFO ProgressMeter - chr13:32370954 15.7 4520 287.6
23:00:28.650 INFO ProgressMeter - chr13:72759793 15.9 4590 288.6
23:00:39.513 INFO ProgressMeter - chr13:102239660 16.1 4660 289.7
23:00:49.658 INFO ProgressMeter - chr13:106286025 16.3 4710 289.7
23:01:00.042 INFO ProgressMeter - chr13:113315499 16.4 4770 290.3
23:01:11.082 INFO ProgressMeter - chr14:36519009 16.6 4820 290.1
23:01:21.670 INFO ProgressMeter - chr14:37595703 16.8 4880 290.6
23:01:32.159 INFO ProgressMeter - chr14:68477946 17.0 4930 290.6
23:01:44.269 INFO ProgressMeter - chr14:95103706 17.2 4980 290.1
23:01:55.392 INFO ProgressMeter - chr14:102085784 17.4 5040 290.5
23:02:09.643 INFO ProgressMeter - chr15:34347752 17.6 5100 289.9
23:02:19.783 INFO ProgressMeter - chr15:40706175 17.8 5140 289.4
23:02:30.507 INFO ProgressMeter - chr15:41736455 17.9 5190 289.3
23:02:40.702 INFO ProgressMeter - chr15:41767076 18.1 5230 288.8
23:02:50.772 INFO ProgressMeter - chr15:66489213 18.3 5290 289.5
23:03:01.604 INFO ProgressMeter - chr15:87977868 18.5 5340 289.3
23:03:13.170 INFO ProgressMeter - chr15:89281168 18.6 5400 289.6
23:03:23.583 INFO ProgressMeter - chr15:90749714 18.8 5460 290.1
23:03:34.700 INFO ProgressMeter - chr15:92953355 19.0 5520 290.4
23:03:45.611 INFO ProgressMeter - chr15:98913042 19.2 5580 290.8
23:03:56.683 INFO ProgressMeter - chr16:2056194 19.4 5640 291.1
23:04:06.792 INFO ProgressMeter - chr16:2175109 19.5 5710 292.2
23:04:16.901 INFO ProgressMeter - chr16:3595603 19.7 5780 293.2
23:04:28.059 INFO ProgressMeter - chr16:3757807 19.9 5830 293.0
23:04:38.627 INFO ProgressMeter - chr16:9798275 20.1 5880 292.9
23:04:50.071 INFO ProgressMeter - chr16:23629202 20.3 5940 293.1
23:05:00.722 INFO ProgressMeter - chr16:50792595 20.4 6000 293.5
23:05:11.401 INFO ProgressMeter - chr16:67621492 20.6 6070 294.4
23:05:24.048 INFO ProgressMeter - chr16:72793897 20.8 6120 293.8
23:05:36.115 INFO ProgressMeter - chr16:72800025 21.0 6160 292.9
23:05:47.156 INFO ProgressMeter - chr16:81889170 21.2 6210 292.7
23:05:57.986 INFO ProgressMeter - chr16:89281934 21.4 6270 293.1
23:06:09.135 INFO ProgressMeter - chr16:89742798 21.6 6320 292.8
23:06:19.357 INFO ProgressMeter - chr17:7314078 21.8 6390 293.8
23:06:30.239 INFO ProgressMeter - chr17:7675557 21.9 6430 293.2
23:06:40.566 INFO ProgressMeter - chr17:12113231 22.1 6500 294.0
23:06:50.940 INFO ProgressMeter - chr17:16121050 22.3 6550 294.0
23:07:02.197 INFO ProgressMeter - chr17:31206238 22.5 6620 294.7
23:07:12.321 INFO ProgressMeter - chr17:31350181 22.6 6680 295.1
23:07:22.519 INFO ProgressMeter - chr17:39471497 22.8 6750 296.0
23:07:33.537 INFO ProgressMeter - chr17:39716299 23.0 6810 296.2
23:07:44.897 INFO ProgressMeter - chr17:40406582 23.2 6880 296.8
23:07:55.872 INFO ProgressMeter - chr17:42322280 23.4 6960 297.9
23:08:07.554 INFO ProgressMeter - chr17:43091805 23.6 7030 298.5
23:08:17.722 INFO ProgressMeter - chr17:43530105 23.7 7080 298.4
23:08:29.111 INFO ProgressMeter - chr17:43536286 23.9 7120 297.7
23:08:41.706 INFO ProgressMeter - chr17:43542476 24.1 7170 297.2
23:08:52.415 INFO ProgressMeter - chr17:43544803 24.3 7190 295.9
23:09:02.724 INFO ProgressMeter - chr17:48727991 24.5 7240 295.8
23:09:13.720 INFO ProgressMeter - chr17:58363334 24.7 7280 295.2
23:09:24.141 INFO ProgressMeter - chr17:59931620 24.8 7350 296.0
23:09:35.020 INFO ProgressMeter - chr17:61793595 25.0 7400 295.8
23:09:45.652 INFO ProgressMeter - chr17:68523723 25.2 7460 296.1
23:09:56.089 INFO ProgressMeter - chr17:80891718 25.4 7530 296.9
23:10:06.405 INFO ProgressMeter - chr18:41962497 25.5 7600 297.6
23:10:16.516 INFO ProgressMeter - chr18:44952377 25.7 7650 297.6
23:10:27.075 INFO ProgressMeter - chr18:58734305 25.9 7710 297.9
23:10:37.362 INFO ProgressMeter - chr19:2189730 26.1 7780 298.6
23:10:48.505 INFO ProgressMeter - chr19:4094451 26.2 7860 299.6
23:10:58.912 INFO ProgressMeter - chr19:5265066 26.4 7930 300.3
23:11:11.996 INFO ProgressMeter - chr19:10154599 26.6 8000 300.4
23:11:22.449 INFO ProgressMeter - chr19:11010379 26.8 8070 301.1
23:11:33.393 INFO ProgressMeter - chr19:14517896 27.0 8140 301.6
23:11:43.719 INFO ProgressMeter - chr19:15184361 27.2 8190 301.6
23:11:55.021 INFO ProgressMeter - chr19:15264402 27.3 8250 301.7
23:12:05.041 INFO ProgressMeter - chr19:19145795 27.5 8320 302.4
23:12:15.717 INFO ProgressMeter - chr19:29819673 27.7 8370 302.3
23:12:26.531 INFO ProgressMeter - chr19:35726234 27.9 8440 302.8
23:12:37.614 INFO ProgressMeter - chr19:40246925 28.1 8510 303.3
23:12:49.702 INFO ProgressMeter - chr19:41260084 28.3 8580 303.6
23:13:00.440 INFO ProgressMeter - chr19:42287948 28.4 8610 302.8
23:13:11.210 INFO ProgressMeter - chr19:45354065 28.6 8670 303.0
23:13:21.331 INFO ProgressMeter - chr19:45413442 28.8 8740 303.6
23:13:32.070 INFO ProgressMeter - chr19:50407059 29.0 8800 303.8
23:13:42.815 INFO ProgressMeter - chr2:15937695 29.1 8850 303.7
23:13:54.655 INFO ProgressMeter - chr2:17772632 29.3 8910 303.7
23:14:06.888 INFO ProgressMeter - chr2:25282598 29.5 8970 303.6
23:14:18.021 INFO ProgressMeter - chr2:29193522 29.7 9020 303.4
23:14:28.838 INFO ProgressMeter - chr2:29224738 29.9 9060 302.9
23:14:38.912 INFO ProgressMeter - chr2:29275097 30.1 9090 302.2
23:14:50.228 INFO ProgressMeter - chr2:42282917 30.3 9140 302.0
23:15:06.882 INFO ProgressMeter - chr2:47416294 30.5 9200 301.2
23:15:17.250 INFO ProgressMeter - chr2:47803550 30.7 9250 301.1
23:15:27.771 INFO ProgressMeter - chr2:61498671 30.9 9320 301.7
23:15:38.285 INFO ProgressMeter - chr2:98552956 31.1 9360 301.3
23:15:49.870 INFO ProgressMeter - chr2:108765057 31.3 9430 301.7
23:15:59.878 INFO ProgressMeter - chr2:111125931 31.4 9480 301.7
23:16:13.034 INFO ProgressMeter - chr2:111130130 31.6 9500 300.2
23:16:24.363 INFO ProgressMeter - chr2:113223483 31.8 9540 299.7
23:16:41.639 INFO ProgressMeter - chr2:113227202 32.1 9570 297.9
23:16:52.257 INFO ProgressMeter - chr2:113231721 32.3 9600 297.2
23:17:03.465 INFO ProgressMeter - chr2:113234064 32.5 9620 296.1
23:17:14.243 INFO ProgressMeter - chr2:127292790 32.7 9680 296.3
23:17:25.688 INFO ProgressMeter - chr2:140492621 32.9 9750 296.7
23:17:37.879 INFO ProgressMeter - chr2:140950233 33.1 9820 297.0
23:17:49.407 INFO ProgressMeter - chr2:172595827 33.3 9880 297.1
23:17:59.914 INFO ProgressMeter - chr2:191146611 33.4 9950 297.7
23:18:09.922 INFO ProgressMeter - chr2:201284954 33.6 10010 298.0
23:18:21.352 INFO ProgressMeter - chr2:214728674 33.8 10080 298.4
23:18:35.228 INFO ProgressMeter - chr2:222201778 34.0 10130 297.8
23:18:48.172 INFO ProgressMeter - chr2:222206432 34.2 10170 297.1
23:19:00.547 INFO ProgressMeter - chr2:222211805 34.4 10210 296.5
23:19:16.735 INFO ProgressMeter - chr2:222216770 34.7 10250 295.3
23:19:28.440 INFO ProgressMeter - chr2:222293628 34.9 10290 294.8
23:19:38.808 INFO ProgressMeter - chr2:226795929 35.1 10350 295.1
23:19:51.039 INFO ProgressMeter - chr20:9580523 35.3 10400 294.8
23:20:02.944 INFO ProgressMeter - chr20:32436402 35.5 10450 294.5
23:20:13.011 INFO ProgressMeter - chr20:37402869 35.6 10510 294.8
23:20:23.867 INFO ProgressMeter - chr20:42771433 35.8 10580 295.3
23:20:36.806 INFO ProgressMeter - chr20:53571742 36.0 10640 295.2
23:20:49.086 INFO ProgressMeter - chr20:58854388 36.2 10690 294.9
23:20:59.432 INFO ProgressMeter - chr21:38380087 36.4 10760 295.4
23:21:10.170 INFO ProgressMeter - chr21:38402555 36.6 10800 295.1
23:21:20.177 INFO ProgressMeter - chr21:41480474 36.8 10840 294.8
23:21:35.057 INFO ProgressMeter - chr21:41491091 37.0 10860 293.4
23:21:46.835 INFO ProgressMeter - chr21:41499408 37.2 10900 292.9
23:21:58.406 INFO ProgressMeter - chr21:41503115 37.4 10930 292.2
23:22:09.292 INFO ProgressMeter - chr21:43093110 37.6 10970 291.9
23:22:20.395 INFO ProgressMeter - chr22:21807662 37.8 11040 292.3
23:22:33.981 INFO ProgressMeter - chr22:23291618 38.0 11080 291.6
23:22:44.325 INFO ProgressMeter - chr22:28715148 38.2 11140 291.9
23:22:55.620 INFO ProgressMeter - chr22:29284974 38.4 11210 292.3
23:23:07.530 INFO ProgressMeter - chr22:29300432 38.6 11240 291.5
23:23:19.167 INFO ProgressMeter - chr22:41157167 38.7 11310 291.9
23:23:31.364 INFO ProgressMeter - chr3:10047915 39.0 11370 291.9
23:23:43.979 INFO ProgressMeter - chr3:12354007 39.2 11440 292.1
23:23:56.945 INFO ProgressMeter - chr3:12358515 39.4 11470 291.3
23:24:08.770 INFO ProgressMeter - chr3:12362232 39.6 11500 290.6
23:24:21.116 INFO ProgressMeter - chr3:12366817 39.8 11540 290.1
23:24:32.065 INFO ProgressMeter - chr3:12371188 40.0 11570 289.5
23:24:43.180 INFO ProgressMeter - chr3:12376076 40.1 11600 288.9
23:24:55.333 INFO ProgressMeter - chr3:12584512 40.4 11640 288.5
23:25:06.332 INFO ProgressMeter - chr3:12653703 40.5 11690 288.4
23:25:17.290 INFO ProgressMeter - chr3:41224952 40.7 11760 288.8
23:25:28.825 INFO ProgressMeter - chr3:47120707 40.9 11820 288.9
23:25:40.257 INFO ProgressMeter - chr3:49685019 41.1 11870 288.8
23:25:50.659 INFO ProgressMeter - chr3:49902616 41.3 11930 289.0
23:26:01.108 INFO ProgressMeter - chr3:52603519 41.4 12000 289.5
23:26:11.695 INFO ProgressMeter - chr3:70972009 41.6 12060 289.7
23:26:23.359 INFO ProgressMeter - chr3:89341753 41.8 12130 290.1
23:26:34.356 INFO ProgressMeter - chr3:135106446 42.0 12190 290.2
23:26:44.896 INFO ProgressMeter - chr3:136464935 42.2 12250 290.4
23:26:56.147 INFO ProgressMeter - chr3:138749912 42.4 12310 290.6
23:27:07.124 INFO ProgressMeter - chr3:142558696 42.5 12380 291.0
23:27:18.379 INFO ProgressMeter - chr3:179210429 42.7 12450 291.3
23:27:29.905 INFO ProgressMeter - chr3:185428877 42.9 12520 291.7
23:27:40.191 INFO ProgressMeter - chr3:186048063 43.1 12560 291.4
23:27:50.367 INFO ProgressMeter - chr3:189864230 43.3 12620 291.7
23:28:01.205 INFO ProgressMeter - chr3:196076091 43.4 12690 292.1
23:28:11.884 INFO ProgressMeter - chr4:20257897 43.6 12760 292.5
23:28:23.608 INFO ProgressMeter - chr4:24570699 43.8 12830 292.8
23:28:34.507 INFO ProgressMeter - chr4:54658013 44.0 12890 292.9
23:28:48.638 INFO ProgressMeter - chr4:54738450 44.2 12940 292.5
23:28:59.889 INFO ProgressMeter - chr4:65490375 44.4 13010 292.8
23:29:10.353 INFO ProgressMeter - chr4:83462467 44.6 13070 293.0
23:29:22.333 INFO ProgressMeter - chr4:105238544 44.8 13130 293.1
23:29:33.209 INFO ProgressMeter - chr4:105275386 45.0 13170 292.8
23:29:43.621 INFO ProgressMeter - chr4:142145902 45.2 13240 293.2
23:29:54.062 INFO ProgressMeter - chr4:186589037 45.3 13300 293.4
23:30:04.756 INFO ProgressMeter - chr4:186617869 45.5 13350 293.4
23:30:14.957 INFO ProgressMeter - chr4:186636777 45.7 13390 293.1
23:30:25.952 INFO ProgressMeter - chr5:235239 45.9 13440 293.1
23:30:37.256 INFO ProgressMeter - chr5:38953459 46.1 13500 293.2
23:30:48.855 INFO ProgressMeter - chr5:44362688 46.2 13570 293.4
23:30:59.755 INFO ProgressMeter - chr5:58454909 46.4 13630 293.6
23:31:10.022 INFO ProgressMeter - chr5:80672251 46.6 13700 294.0
23:31:20.888 INFO ProgressMeter - chr5:112815517 46.8 13780 294.6
23:31:31.337 INFO ProgressMeter - chr5:112840922 47.0 13820 294.3
23:31:43.362 INFO ProgressMeter - chr5:122450940 47.2 13870 294.2
23:31:54.578 INFO ProgressMeter - chr5:138929244 47.3 13940 294.5
23:32:06.822 INFO ProgressMeter - chr5:142697259 47.5 14000 294.5
23:32:17.359 INFO ProgressMeter - chr5:150115761 47.7 14060 294.6
23:32:28.390 INFO ProgressMeter - chr5:150403861 47.9 14120 294.8
23:32:39.482 INFO ProgressMeter - chr5:177089601 48.1 14190 295.1
23:32:50.757 INFO ProgressMeter - chr5:177097525 48.3 14230 294.8
23:33:02.208 INFO ProgressMeter - chr5:177211460 48.5 14260 294.2
23:33:13.282 INFO ProgressMeter - chr5:177515908 48.7 14320 294.3
23:33:24.548 INFO ProgressMeter - chr6:12059696 48.8 14390 294.6
23:33:35.261 INFO ProgressMeter - chr6:20484051 49.0 14460 295.0
23:33:45.350 INFO ProgressMeter - chr6:26271324 49.2 14530 295.4
23:33:55.869 INFO ProgressMeter - chr6:30704385 49.4 14560 295.0
23:34:06.207 INFO ProgressMeter - chr6:32200829 49.5 14610 295.0
23:34:16.282 INFO ProgressMeter - chr6:32223003 49.7 14660 295.0
23:34:26.340 INFO ProgressMeter - chr6:41936557 49.9 14720 295.2
23:34:37.377 INFO ProgressMeter - chr6:93254645 50.1 14800 295.7
23:34:47.890 INFO ProgressMeter - chr6:111699513 50.2 14860 295.9
23:34:59.548 INFO ProgressMeter - chr6:117320487 50.4 14910 295.7
23:35:11.736 INFO ProgressMeter - chr6:117324451 50.6 14940 295.1
23:35:22.828 INFO ProgressMeter - chr6:117330379 50.8 14980 294.8
23:35:35.880 INFO ProgressMeter - chr6:117338502 51.0 15030 294.5
23:35:47.345 INFO ProgressMeter - chr6:117385681 51.2 15080 294.4
23:35:59.270 INFO ProgressMeter - chr6:135204297 51.4 15140 294.5
23:36:12.039 INFO ProgressMeter - chr6:135208601 51.6 15180 294.0
23:36:28.899 INFO ProgressMeter - chr6:135212911 51.9 15210 293.0
23:36:39.295 INFO ProgressMeter - chr6:135216018 52.1 15240 292.6
23:36:49.872 INFO ProgressMeter - chr6:137878897 52.3 15290 292.6
23:37:01.731 INFO ProgressMeter - chr6:151366427 52.5 15340 292.4
23:37:12.427 INFO ProgressMeter - chr6:152061323 52.6 15390 292.4
23:37:22.468 INFO ProgressMeter - chr6:157196163 52.8 15440 292.4
23:37:33.739 INFO ProgressMeter - chr6:161092008 53.0 15490 292.3
23:37:45.410 INFO ProgressMeter - chr7:2926737 53.2 15570 292.7
23:37:56.572 INFO ProgressMeter - chr7:13892427 53.4 15630 292.9
23:38:07.441 INFO ProgressMeter - chr7:13907627 53.6 15670 292.6
23:38:19.018 INFO ProgressMeter - chr7:13933202 53.7 15700 292.1
23:38:29.276 INFO ProgressMeter - chr7:13938172 53.9 15740 291.9
23:38:42.817 INFO ProgressMeter - chr7:13942384 54.1 15770 291.3
23:38:54.894 INFO ProgressMeter - chr7:13946062 54.3 15800 290.7
23:39:05.661 INFO ProgressMeter - chr7:13950012 54.5 15830 290.3
23:39:21.546 INFO ProgressMeter - chr7:13953726 54.8 15860 289.5
23:39:37.201 INFO ProgressMeter - chr7:13960004 55.0 15910 289.0
23:39:52.744 INFO ProgressMeter - chr7:13964567 55.3 15940 288.2
23:40:03.544 INFO ProgressMeter - chr7:13969712 55.5 15980 288.0
23:40:13.635 INFO ProgressMeter - chr7:13970886 55.7 15990 287.3
23:40:24.916 INFO ProgressMeter - chr7:13974705 55.8 16020 286.9
23:40:36.725 INFO ProgressMeter - chr7:13978245 56.0 16040 286.2
23:40:46.863 INFO ProgressMeter - chr7:13982167 56.2 16070 285.9
23:41:04.114 INFO ProgressMeter - chr7:13988727 56.5 16110 285.1
23:41:16.083 INFO ProgressMeter - chr7:55152758 56.7 16170 285.2
23:41:30.575 INFO ProgressMeter - chr7:55167910 56.9 16220 284.9
23:41:42.303 INFO ProgressMeter - chr7:55177334 57.1 16260 284.6
23:41:52.891 INFO ProgressMeter - chr7:55191717 57.3 16300 284.4
23:42:04.412 INFO ProgressMeter - chr7:78489759 57.5 16360 284.5
23:42:14.784 INFO ProgressMeter - chr7:92618070 57.7 16420 284.7
23:42:26.301 INFO ProgressMeter - chr7:102197017 57.9 16490 285.0
23:42:37.641 INFO ProgressMeter - chr7:106868600 58.1 16550 285.1
23:42:48.042 INFO ProgressMeter - chr7:116759430 58.2 16600 285.1
23:42:59.809 INFO ProgressMeter - chr7:140738901 58.4 16660 285.1
23:43:10.720 INFO ProgressMeter - chr7:140789558 58.6 16690 284.8
23:43:22.108 INFO ProgressMeter - chr7:140833203 58.8 16740 284.7
23:43:33.562 INFO ProgressMeter - chr7:148827162 59.0 16820 285.1
23:43:44.568 INFO ProgressMeter - chr7:152162743 59.2 16880 285.3
23:43:55.096 INFO ProgressMeter - chr7:152181801 59.3 16920 285.1
23:44:06.405 INFO ProgressMeter - chr7:152660699 59.5 16990 285.4
23:44:17.515 INFO ProgressMeter - chr8:32412130 59.7 17070 285.8
23:44:27.907 INFO ProgressMeter - chr8:32754370 59.9 17110 285.7
23:44:39.013 INFO ProgressMeter - chr8:37840758 60.1 17180 286.0
23:44:50.477 INFO ProgressMeter - chr8:38457354 60.3 17240 286.0
23:45:01.209 INFO ProgressMeter - chr8:41974789 60.4 17290 286.0
23:45:12.299 INFO ProgressMeter - chr8:47837282 60.6 17350 286.1
23:45:23.310 INFO ProgressMeter - chr8:47939549 60.8 17420 286.4
23:45:33.520 INFO ProgressMeter - chr8:68077395 61.0 17490 286.8
23:45:43.775 INFO ProgressMeter - chr8:89955539 61.2 17550 287.0
23:45:54.565 INFO ProgressMeter - chr8:127731415 61.3 17610 287.1
23:46:05.776 INFO ProgressMeter - chr8:127742934 61.5 17660 287.0
23:46:16.505 INFO ProgressMeter - chr9:5054861 61.7 17730 287.3
23:46:27.700 INFO ProgressMeter - chr9:8389230 61.9 17800 287.6
23:46:39.680 INFO ProgressMeter - chr9:20456702 62.1 17860 287.6
23:46:51.116 INFO ProgressMeter - chr9:36966547 62.3 17930 287.9
23:47:01.902 INFO ProgressMeter - chr9:84727705 62.5 17990 288.0
23:47:12.413 INFO ProgressMeter - chr9:84744665 62.6 18010 287.5
23:47:23.218 INFO ProgressMeter - chr9:84813738 62.8 18040 287.2
23:47:33.581 INFO ProgressMeter - chr9:84862096 63.0 18060 286.7
23:47:45.866 INFO ProgressMeter - chr9:84865619 63.2 18090 286.3
23:47:57.616 INFO ProgressMeter - chr9:84875930 63.4 18130 286.0
23:48:09.714 INFO ProgressMeter - chr9:85023944 63.6 18170 285.7
23:48:20.969 INFO ProgressMeter - chr9:90878949 63.8 18210 285.5
23:48:31.187 INFO ProgressMeter - chr9:95477545 63.9 18270 285.7
23:48:42.761 INFO ProgressMeter - chr9:125188917 64.1 18340 285.9
23:48:54.774 INFO ProgressMeter - chr9:130887567 64.3 18390 285.8
23:49:05.498 INFO ProgressMeter - chr9:136502270 64.5 18450 286.0
23:49:15.855 INFO ProgressMeter - chr9:136921091 64.7 18520 286.3
23:49:26.103 INFO ProgressMeter - chrX:45090721 64.9 18630 287.2
23:49:36.515 INFO ProgressMeter - chrX:49035920 65.0 18730 288.0
23:49:46.730 INFO ProgressMeter - chrX:53396206 65.2 18820 288.6
23:49:59.196 INFO ProgressMeter - chrX:67546076 65.4 18890 288.8
23:50:10.507 INFO ProgressMeter - chrX:71142173 65.6 19000 289.6
23:50:21.058 INFO ProgressMeter - chrX:77683131 65.8 19100 290.4
23:50:32.456 INFO ProgressMeter - chrX:130015136 66.0 19230 291.5
23:50:41.895 INFO Mutect2 - 810006 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
138 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
810144 total reads filtered out of 118874166 reads processed
23:50:41.895 INFO ProgressMeter - chrY:21207450 66.1 19330 292.3
23:50:41.895 INFO ProgressMeter - Traversal complete. Processed 19330 total regions in 66.1 minutes.
23:50:41.911 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.597056848
23:50:41.911 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 357.76015828000004
23:50:41.911 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 11.92 sec
23:50:41.911 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:50:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 66.14 minutes.
Runtime.totalMemory()=3640655872
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 LS0893_tumor.bam --tumor-sample LS0893 -L TST500C_manifest.bed -O LS0893.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:50:43.278 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
23:50:43.400 INFO FilterMutectCalls - ------------------------------------------------------------
23:50:43.403 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:50:43.403 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:50:43.403 INFO FilterMutectCalls - Executing as ?@nf-0eec2f26c2c2964db6ffbccd08442747-54705-hbpq2 on Linux v6.12.88 amd64
23:50:43.403 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:50:43.403 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:50:43 PM GMT
23:50:43.404 INFO FilterMutectCalls - ------------------------------------------------------------
23:50:43.404 INFO FilterMutectCalls - ------------------------------------------------------------
23:50:43.404 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:50:43.404 INFO FilterMutectCalls - Picard Version: 3.1.1
23:50:43.404 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:50:43.404 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:50:43.404 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:50:43.405 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:50:43.405 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:50:43.405 INFO FilterMutectCalls - Deflater: IntelDeflater
23:50:43.405 INFO FilterMutectCalls - Inflater: IntelInflater
23:50:43.405 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:50:43.405 INFO FilterMutectCalls - Requester pays: disabled
23:50:43.405 INFO FilterMutectCalls - Initializing engine
23:50:43.591 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.UVjpXjoRSs/LS0893.mutect2.raw.vcf.gz
23:50:43.702 INFO FilterMutectCalls - Done initializing engine
23:50:43.758 INFO ProgressMeter - Starting traversal
23:50:43.758 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:50:43.759 INFO FilterMutectCalls - Starting pass 0 through the variants
23:50:45.462 INFO FilterMutectCalls - Finished pass 0 through the variants
23:50:47.042 INFO FilterMutectCalls - Starting pass 1 through the variants
23:50:48.797 INFO FilterMutectCalls - Finished pass 1 through the variants
23:50:49.223 INFO FilterMutectCalls - Starting pass 2 through the variants
23:50:50.930 INFO FilterMutectCalls - Finished pass 2 through the variants
23:50:50.932 INFO FilterMutectCalls - Starting pass 3 through the variants
23:50:52.347 INFO FilterMutectCalls - Finished pass 3 through the variants
23:50:52.360 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:50:52.361 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:50:52.361 INFO ProgressMeter - chr7:13952562 0.1 10440 72811.8
23:50:52.361 INFO ProgressMeter - Traversal complete. Processed 10440 total variants in 0.1 minutes.
23:50:52.372 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:50:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=469762048
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 LS0893.mutect2.raw.vcf.gz --stats LS0893.mutect2.raw.vcf.gz.stats -O LS0893.mutect2.filtered.vcf.gz
23:50:53.498 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
23:50:53.571 INFO SelectVariants - ------------------------------------------------------------
23:50:53.573 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:50:53.573 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:50:53.573 INFO SelectVariants - Executing as ?@nf-0eec2f26c2c2964db6ffbccd08442747-54705-hbpq2 on Linux v6.12.88 amd64
23:50:53.573 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:50:53.573 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:50:53 PM GMT
23:50:53.573 INFO SelectVariants - ------------------------------------------------------------
23:50:53.573 INFO SelectVariants - ------------------------------------------------------------
23:50:53.574 INFO SelectVariants - HTSJDK Version: 4.1.0
23:50:53.574 INFO SelectVariants - Picard Version: 3.1.1
23:50:53.574 INFO SelectVariants - Built for Spark Version: 3.5.0
23:50:53.574 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:50:53.574 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:50:53.574 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:50:53.574 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:50:53.574 INFO SelectVariants - Deflater: IntelDeflater
23:50:53.574 INFO SelectVariants - Inflater: IntelInflater
23:50:53.574 INFO SelectVariants - GCS max retries/reopens: 20
23:50:53.574 INFO SelectVariants - Requester pays: disabled
23:50:53.575 INFO SelectVariants - Initializing engine
23:50:53.683 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.UVjpXjoRSs/LS0893.mutect2.filtered.vcf.gz
23:50:53.773 INFO SelectVariants - Done initializing engine
23:50:53.805 INFO ProgressMeter - Starting traversal
23:50:53.805 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:50:53.873 INFO ProgressMeter - chr6:135208081 0.0 2610 2337313.4
23:50:53.873 INFO ProgressMeter - Traversal complete. Processed 2610 total variants in 0.0 minutes.
23:50:53.883 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:50:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=511705088
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 LS0893.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0893.mutect2.pass.vcf.gz