Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/43/03c72a5dcb245e61eedf73e583d348/.command.sh
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa.fai
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/TSO500/TST500C_manifest.bed
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz.tbi
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/43/03c72a5dcb245e61eedf73e583d348/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0906/LS0906_tumor.bam
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0906/LS0906_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:34.287 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
22:44:34.421 INFO Mutect2 - ------------------------------------------------------------
22:44:34.424 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:34.424 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:34.424 INFO Mutect2 - Executing as ?@nf-4303c72a5dcb245e61eedf73e583d348-4a883-2tvxx on Linux v6.12.88 amd64
22:44:34.425 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:34.425 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:34 PM GMT
22:44:34.425 INFO Mutect2 - ------------------------------------------------------------
22:44:34.425 INFO Mutect2 - ------------------------------------------------------------
22:44:34.426 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:34.426 INFO Mutect2 - Picard Version: 3.1.1
22:44:34.426 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:34.427 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:34.427 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:34.427 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:34.427 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:34.427 INFO Mutect2 - Deflater: IntelDeflater
22:44:34.427 INFO Mutect2 - Inflater: IntelInflater
22:44:34.427 INFO Mutect2 - GCS max retries/reopens: 20
22:44:34.427 INFO Mutect2 - Requester pays: disabled
22:44:34.428 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.NG6PoaAekz/LS0906_tumor.bam.bai is older than BAM /tmp/nxf.NG6PoaAekz/LS0906_tumor.bam
22:44:34.652 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.NG6PoaAekz/af-only-gnomad.hg38.vcf.gz
22:44:34.788 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.NG6PoaAekz/TST500C_manifest.bed
22:44:34.829 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:34.859 INFO Mutect2 - Done initializing engine
22:44:34.870 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
22:44:34.873 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
22:44:34.874 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:34.874 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:34.886 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
22:44:34.895 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:34.895 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:34.896 INFO IntelPairHmm - Available threads: 384
22:44:34.896 INFO IntelPairHmm - Requested threads: 4
22:44:34.896 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:34.934 INFO ProgressMeter - Starting traversal
22:44:34.934 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:46.046 INFO ProgressMeter - chr1:9722015 0.2 50 270.0
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22:48:10.335 INFO ProgressMeter - chr1:204557071 3.6 1190 331.5
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22:48:31.392 INFO ProgressMeter - chr1:243503059 3.9 1310 332.4
22:48:43.359 INFO ProgressMeter - chr10:27014714 4.1 1370 330.9
22:48:53.820 INFO ProgressMeter - chr10:27100324 4.3 1430 331.4
22:49:05.951 INFO ProgressMeter - chr10:43109029 4.5 1500 332.1
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22:49:39.246 INFO ProgressMeter - chr10:68644979 5.1 1630 321.4
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22:50:23.823 INFO ProgressMeter - chr10:121479879 5.8 1890 325.0
22:50:33.856 INFO ProgressMeter - chr10:121483304 6.0 1920 321.0
22:50:44.834 INFO ProgressMeter - chr11:533275 6.2 1980 321.2
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22:51:25.713 INFO ProgressMeter - chr11:69773617 6.8 2240 327.2
22:51:38.336 INFO ProgressMeter - chr11:69810832 7.1 2280 323.1
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22:52:33.131 INFO ProgressMeter - chr11:102330997 8.0 2540 318.7
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22:53:40.118 INFO ProgressMeter - chr11:128489292 9.1 2850 313.7
22:53:50.143 INFO ProgressMeter - chr11:128813124 9.3 2890 312.3
22:54:01.191 INFO ProgressMeter - chr12:4367527 9.4 2960 313.6
22:54:11.335 INFO ProgressMeter - chr12:4433341 9.6 3020 314.4
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22:55:08.633 INFO ProgressMeter - chr12:11867721 10.6 3250 307.7
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22:55:29.377 INFO ProgressMeter - chr12:25248016 10.9 3370 309.0
22:55:39.914 INFO ProgressMeter - chr12:45851295 11.1 3420 308.6
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22:56:05.163 INFO ProgressMeter - chr12:49038583 11.5 3520 306.0
22:56:15.297 INFO ProgressMeter - chr12:49050895 11.7 3570 305.8
22:56:25.916 INFO ProgressMeter - chr12:56083889 11.8 3640 307.2
22:56:36.891 INFO ProgressMeter - chr12:57092251 12.0 3710 308.3
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22:57:31.324 INFO ProgressMeter - chr12:132649738 12.9 4020 310.7
22:57:41.776 INFO ProgressMeter - chr13:20988562 13.1 4080 311.1
22:57:52.066 INFO ProgressMeter - chr13:21800508 13.3 4150 312.4
22:58:02.556 INFO ProgressMeter - chr13:28322788 13.5 4220 313.5
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22:58:37.883 INFO ProgressMeter - chr13:32357740 14.0 4370 311.1
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22:59:09.914 INFO ProgressMeter - chr13:113304196 14.6 4600 315.4
22:59:21.141 INFO ProgressMeter - chr14:35402494 14.8 4650 314.8
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22:59:42.077 INFO ProgressMeter - chr14:80955679 15.1 4790 316.8
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23:00:05.495 INFO ProgressMeter - chr15:34345855 15.5 4920 317.2
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23:01:13.201 INFO ProgressMeter - chr15:90749769 16.6 5290 318.0
23:01:23.647 INFO ProgressMeter - chr15:92984328 16.8 5350 318.2
23:01:33.970 INFO ProgressMeter - chr16:288120 17.0 5410 318.5
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23:02:41.279 INFO ProgressMeter - chr16:50779875 18.1 5800 320.3
23:02:52.290 INFO ProgressMeter - chr16:67636688 18.3 5870 321.0
23:03:05.230 INFO ProgressMeter - chr16:72793897 18.5 5920 319.9
23:03:16.000 INFO ProgressMeter - chr16:72797784 18.7 5950 318.4
23:03:26.769 INFO ProgressMeter - chr16:81880908 18.9 5990 317.5
23:03:37.492 INFO ProgressMeter - chr16:89281687 19.0 6050 317.7
23:03:48.514 INFO ProgressMeter - chr16:89316931 19.2 6090 316.8
23:04:00.494 INFO ProgressMeter - chr17:7669607 19.4 6170 317.6
23:04:10.893 INFO ProgressMeter - chr17:8081104 19.6 6240 318.4
23:04:22.561 INFO ProgressMeter - chr17:16101521 19.8 6320 319.3
23:04:32.664 INFO ProgressMeter - chr17:31214449 20.0 6400 320.6
23:04:42.979 INFO ProgressMeter - chr17:31947615 20.1 6470 321.3
23:04:54.230 INFO ProgressMeter - chr17:39699558 20.3 6540 321.8
23:05:05.827 INFO ProgressMeter - chr17:40389517 20.5 6610 322.2
23:05:16.244 INFO ProgressMeter - chr17:42295617 20.7 6690 323.4
23:05:26.269 INFO ProgressMeter - chr17:43070926 20.9 6760 324.1
23:05:37.204 INFO ProgressMeter - chr17:43113664 21.0 6810 323.7
23:05:47.874 INFO ProgressMeter - chr17:43534540 21.2 6860 323.3
23:05:59.504 INFO ProgressMeter - chr17:43541537 21.4 6910 322.8
23:06:10.309 INFO ProgressMeter - chr17:43546431 21.6 6940 321.5
23:06:21.342 INFO ProgressMeter - chr17:58357992 21.8 7000 321.5
23:06:31.627 INFO ProgressMeter - chr17:59934432 21.9 7070 322.2
23:06:42.650 INFO ProgressMeter - chr17:61793595 22.1 7120 321.8
23:06:53.647 INFO ProgressMeter - chr17:68515444 22.3 7180 321.8
23:07:03.880 INFO ProgressMeter - chr17:80957622 22.5 7250 322.5
23:07:15.344 INFO ProgressMeter - chr18:44869209 22.7 7330 323.3
23:07:26.668 INFO ProgressMeter - chr18:45063454 22.9 7370 322.4
23:07:38.498 INFO ProgressMeter - chr18:63318476 23.1 7450 323.1
23:07:49.957 INFO ProgressMeter - chr19:2226894 23.3 7540 324.3
23:08:01.207 INFO ProgressMeter - chr19:5222897 23.4 7620 325.1
23:08:11.725 INFO ProgressMeter - chr19:10136119 23.6 7690 325.7
23:08:22.253 INFO ProgressMeter - chr19:10486650 23.8 7750 325.8
23:08:33.101 INFO ProgressMeter - chr19:11059810 24.0 7820 326.2
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23:08:53.793 INFO ProgressMeter - chr19:15243136 24.3 7940 326.6
23:09:03.827 INFO ProgressMeter - chr19:18161443 24.5 8010 327.2
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23:09:34.853 INFO ProgressMeter - chr19:40235043 25.0 8200 328.0
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23:10:26.887 INFO ProgressMeter - chr19:52222097 25.9 8520 329.4
23:10:37.430 INFO ProgressMeter - chr2:15944586 26.0 8560 328.7
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23:11:00.146 INFO ProgressMeter - chr2:25753532 26.4 8670 328.2
23:11:11.257 INFO ProgressMeter - chr2:29222802 26.6 8730 328.1
23:11:24.794 INFO ProgressMeter - chr2:29228942 26.8 8770 326.9
23:11:35.322 INFO ProgressMeter - chr2:42282821 27.0 8830 327.0
23:11:45.419 INFO ProgressMeter - chr2:47403190 27.2 8880 326.8
23:11:56.803 INFO ProgressMeter - chr2:47799108 27.4 8920 326.0
23:12:08.193 INFO ProgressMeter - chr2:61483935 27.6 8990 326.3
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23:12:29.776 INFO ProgressMeter - chr2:108764077 27.9 9100 326.0
23:12:40.365 INFO ProgressMeter - chr2:111127052 28.1 9150 325.7
23:12:51.977 INFO ProgressMeter - chr2:111161417 28.3 9170 324.2
23:13:06.187 INFO ProgressMeter - chr2:113224916 28.5 9210 322.9
23:13:17.212 INFO ProgressMeter - chr2:113228455 28.7 9240 321.9
23:13:31.635 INFO ProgressMeter - chr2:113233071 28.9 9280 320.6
23:13:42.944 INFO ProgressMeter - chr2:127272863 29.1 9320 319.9
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23:14:38.023 INFO ProgressMeter - chr2:211383952 30.1 9670 321.8
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23:15:11.299 INFO ProgressMeter - chr2:222208538 30.6 9800 320.2
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23:16:06.326 INFO ProgressMeter - chr20:32429992 31.5 10030 318.2
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23:16:39.493 INFO ProgressMeter - chr20:52679538 32.1 10220 318.6
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23:17:00.949 INFO ProgressMeter - chr21:38381097 32.4 10340 318.8
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23:17:22.664 INFO ProgressMeter - chr21:41489903 32.8 10430 318.0
23:17:36.700 INFO ProgressMeter - chr21:41492819 33.0 10450 316.4
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23:18:00.487 INFO ProgressMeter - chr21:41506721 33.4 10530 315.0
23:18:11.501 INFO ProgressMeter - chr22:20996694 33.6 10600 315.4
23:18:27.287 INFO ProgressMeter - chr22:23292193 33.9 10660 314.7
23:18:38.098 INFO ProgressMeter - chr22:28730418 34.1 10740 315.4
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23:19:00.135 INFO ProgressMeter - chr22:33163560 34.4 10840 314.9
23:19:11.833 INFO ProgressMeter - chr22:41177780 34.6 10910 315.2
23:19:22.494 INFO ProgressMeter - chr3:12288935 34.8 10980 315.6
23:19:33.971 INFO ProgressMeter - chr3:12356834 35.0 11020 315.0
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23:20:08.384 INFO ProgressMeter - chr3:12372567 35.6 11130 313.0
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23:22:54.900 INFO ProgressMeter - chr3:196055078 38.3 12120 316.2
23:23:05.355 INFO ProgressMeter - chr4:1803607 38.5 12200 316.8
23:23:17.063 INFO ProgressMeter - chr4:24529643 38.7 12280 317.3
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23:25:49.159 INFO ProgressMeter - chr5:44388679 41.2 13080 317.2
23:26:00.236 INFO ProgressMeter - chr5:58455623 41.4 13120 316.7
23:26:10.701 INFO ProgressMeter - chr5:80854128 41.6 13200 317.3
23:26:22.708 INFO ProgressMeter - chr5:112839410 41.8 13280 317.7
23:26:32.853 INFO ProgressMeter - chr5:122423107 42.0 13320 317.4
23:26:43.510 INFO ProgressMeter - chr5:137297687 42.1 13380 317.5
23:26:55.330 INFO ProgressMeter - chr5:142672767 42.3 13450 317.7
23:27:05.660 INFO ProgressMeter - chr5:150070231 42.5 13500 317.6
23:27:16.388 INFO ProgressMeter - chr5:150401935 42.7 13560 317.6
23:27:28.083 INFO ProgressMeter - chr5:177088819 42.9 13630 317.8
23:27:39.096 INFO ProgressMeter - chr5:177096285 43.1 13670 317.4
23:27:51.065 INFO ProgressMeter - chr5:177238235 43.3 13710 316.9
23:28:03.065 INFO ProgressMeter - chr5:177516704 43.5 13770 316.8
23:28:15.182 INFO ProgressMeter - chr6:401629 43.7 13830 316.7
23:28:27.122 INFO ProgressMeter - chr6:20482760 43.9 13900 316.8
23:28:38.730 INFO ProgressMeter - chr6:26271272 44.1 13970 317.0
23:28:50.488 INFO ProgressMeter - chr6:30704528 44.3 14000 316.3
23:29:01.705 INFO ProgressMeter - chr6:32197404 44.4 14050 316.1
23:29:14.213 INFO ProgressMeter - chr6:33319564 44.7 14110 316.0
23:29:24.303 INFO ProgressMeter - chr6:41936557 44.8 14170 316.1
23:29:35.065 INFO ProgressMeter - chr6:43780767 45.0 14240 316.4
23:29:45.730 INFO ProgressMeter - chr6:106105893 45.2 14300 316.5
23:29:55.931 INFO ProgressMeter - chr6:117318750 45.3 14350 316.4
23:30:06.299 INFO ProgressMeter - chr6:117323318 45.5 14380 315.9
23:30:18.391 INFO ProgressMeter - chr6:117330579 45.7 14430 315.6
23:30:28.905 INFO ProgressMeter - chr6:117338914 45.9 14480 315.5
23:30:39.971 INFO ProgressMeter - chr6:117416256 46.1 14540 315.5
23:30:50.222 INFO ProgressMeter - chr6:135206568 46.3 14590 315.4
23:31:10.077 INFO ProgressMeter - chr6:135213230 46.6 14630 314.0
23:31:20.703 INFO ProgressMeter - chr6:137200879 46.8 14670 313.7
23:31:31.619 INFO ProgressMeter - chr6:149684269 46.9 14730 313.8
23:31:43.388 INFO ProgressMeter - chr6:151956640 47.1 14780 313.5
23:31:53.532 INFO ProgressMeter - chr6:157167133 47.3 14830 313.5
23:32:04.205 INFO ProgressMeter - chr6:161070606 47.5 14880 313.3
23:32:15.762 INFO ProgressMeter - chr7:2924261 47.7 14960 313.8
23:32:28.430 INFO ProgressMeter - chr7:13894066 47.9 15030 313.8
23:32:43.754 INFO ProgressMeter - chr7:13931921 48.1 15070 313.0
23:32:55.221 INFO ProgressMeter - chr7:13938094 48.3 15110 312.6
23:33:06.152 INFO ProgressMeter - chr7:13944288 48.5 15150 312.2
23:33:19.166 INFO ProgressMeter - chr7:13949089 48.7 15180 311.5
23:33:30.734 INFO ProgressMeter - chr7:13952700 48.9 15210 310.9
23:33:41.491 INFO ProgressMeter - chr7:13957251 49.1 15240 310.3
23:33:54.013 INFO ProgressMeter - chr7:13962396 49.3 15270 309.6
23:34:05.056 INFO ProgressMeter - chr7:13966761 49.5 15300 309.1
23:34:18.167 INFO ProgressMeter - chr7:13973141 49.7 15340 308.5
23:34:33.027 INFO ProgressMeter - chr7:13977083 50.0 15370 307.6
23:34:46.107 INFO ProgressMeter - chr7:13983209 50.2 15410 307.1
23:34:58.608 INFO ProgressMeter - chr7:13988907 50.4 15440 306.4
23:35:10.571 INFO ProgressMeter - chr7:55151293 50.6 15500 306.4
23:35:24.278 INFO ProgressMeter - chr7:55168029 50.8 15550 306.0
23:35:35.835 INFO ProgressMeter - chr7:55175158 51.0 15580 305.4
23:35:47.794 INFO ProgressMeter - chr7:55179776 51.2 15620 305.0
23:35:59.100 INFO ProgressMeter - chr7:78127367 51.4 15670 304.8
23:36:10.335 INFO ProgressMeter - chr7:86839480 51.6 15740 305.1
23:36:20.898 INFO ProgressMeter - chr7:102201339 51.8 15820 305.6
23:36:33.441 INFO ProgressMeter - chr7:116699984 52.0 15890 305.7
23:36:44.677 INFO ProgressMeter - chr7:129210361 52.2 15950 305.8
23:36:56.677 INFO ProgressMeter - chr7:140793361 52.4 16010 305.8
23:37:07.267 INFO ProgressMeter - chr7:148809069 52.5 16090 306.2
23:37:17.462 INFO ProgressMeter - chr7:152162232 52.7 16160 306.6
23:37:27.767 INFO ProgressMeter - chr7:152181564 52.9 16200 306.4
23:37:38.804 INFO ProgressMeter - chr7:152648892 53.1 16270 306.6
23:37:49.479 INFO ProgressMeter - chr8:32293130 53.2 16350 307.1
23:38:01.826 INFO ProgressMeter - chr8:32763216 53.4 16400 306.8
23:38:12.326 INFO ProgressMeter - chr8:38415868 53.6 16470 307.1
23:38:22.398 INFO ProgressMeter - chr8:41932868 53.8 16530 307.3
23:38:32.399 INFO ProgressMeter - chr8:47777684 54.0 16580 307.3
23:38:43.840 INFO ProgressMeter - chr8:47881414 54.1 16640 307.3
23:38:54.910 INFO ProgressMeter - chr8:55946446 54.3 16710 307.5
23:39:05.475 INFO ProgressMeter - chr8:68192333 54.5 16770 307.7
23:39:16.346 INFO ProgressMeter - chr8:116858350 54.7 16840 307.9
23:39:27.946 INFO ProgressMeter - chr8:127740151 54.9 16890 307.7
23:39:38.654 INFO ProgressMeter - chr9:5015244 55.1 16950 307.8
23:39:49.448 INFO ProgressMeter - chr9:8376605 55.2 17030 308.3
23:40:00.809 INFO ProgressMeter - chr9:21968573 55.4 17100 308.5
23:40:11.932 INFO ProgressMeter - chr9:83971861 55.6 17180 308.9
23:40:23.378 INFO ProgressMeter - chr9:84742864 55.8 17230 308.7
23:40:35.818 INFO ProgressMeter - chr9:84814527 56.0 17270 308.3
23:40:47.070 INFO ProgressMeter - chr9:84863748 56.2 17300 307.8
23:40:58.085 INFO ProgressMeter - chr9:84873089 56.4 17330 307.3
23:41:10.577 INFO ProgressMeter - chr9:85022268 56.6 17380 307.1
23:41:22.240 INFO ProgressMeter - chr9:90862204 56.8 17420 306.8
23:41:32.504 INFO ProgressMeter - chr9:95476114 57.0 17480 306.9
23:41:42.701 INFO ProgressMeter - chr9:125171083 57.1 17550 307.2
23:41:54.545 INFO ProgressMeter - chr9:132896233 57.3 17610 307.2
23:42:05.843 INFO ProgressMeter - chr9:136506595 57.5 17680 307.4
23:42:17.481 INFO ProgressMeter - chrX:20130514 57.7 17770 307.9
23:42:28.146 INFO ProgressMeter - chrX:45060607 57.9 17830 308.0
23:42:38.265 INFO ProgressMeter - chrX:47563224 58.1 17890 308.2
23:42:48.432 INFO ProgressMeter - chrX:49034452 58.2 17940 308.1
23:42:58.846 INFO ProgressMeter - chrX:49037771 58.4 17970 307.7
23:43:10.158 INFO ProgressMeter - chrX:53214848 58.6 18030 307.7
23:43:21.627 INFO ProgressMeter - chrX:53414786 58.8 18080 307.6
23:43:34.345 INFO ProgressMeter - chrX:67545609 59.0 18120 307.2
23:43:45.461 INFO ProgressMeter - chrX:71120969 59.2 18180 307.2
23:43:55.551 INFO ProgressMeter - chrX:71140633 59.3 18240 307.4
23:44:06.040 INFO ProgressMeter - chrX:71459550 59.5 18290 307.3
23:44:17.946 INFO ProgressMeter - chrX:77682700 59.7 18350 307.3
23:44:29.240 INFO ProgressMeter - chrX:123885958 59.9 18420 307.5
23:44:40.078 INFO ProgressMeter - chrX:130013727 60.1 18490 307.7
23:44:50.640 INFO ProgressMeter - chrY:2944905 60.3 18540 307.7
23:44:50.654 INFO Mutect2 - 739233 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
4 read(s) filtered by: ReadLengthReadFilter
199 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
739436 total reads filtered out of 105962718 reads processed
23:44:50.654 INFO ProgressMeter - chrY:19564390 60.3 18579 308.3
23:44:50.654 INFO ProgressMeter - Traversal complete. Processed 18579 total regions in 60.3 minutes.
23:44:50.670 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.001234404000001
23:44:50.670 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 293.038370781
23:44:50.671 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 10.79 sec
23:44:50.671 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:44:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 60.27 minutes.
Runtime.totalMemory()=6450839552
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 LS0906_tumor.bam --tumor-sample LS0906 -L TST500C_manifest.bed -O LS0906.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:44:52.763 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
23:44:52.885 INFO FilterMutectCalls - ------------------------------------------------------------
23:44:52.887 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:44:52.888 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:44:52.888 INFO FilterMutectCalls - Executing as ?@nf-4303c72a5dcb245e61eedf73e583d348-4a883-2tvxx on Linux v6.12.88 amd64
23:44:52.888 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:44:52.888 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:44:52 PM GMT
23:44:52.888 INFO FilterMutectCalls - ------------------------------------------------------------
23:44:52.888 INFO FilterMutectCalls - ------------------------------------------------------------
23:44:52.889 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:44:52.889 INFO FilterMutectCalls - Picard Version: 3.1.1
23:44:52.889 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:44:52.889 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:44:52.890 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:44:52.890 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:44:52.890 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:44:52.890 INFO FilterMutectCalls - Deflater: IntelDeflater
23:44:52.890 INFO FilterMutectCalls - Inflater: IntelInflater
23:44:52.890 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:44:52.890 INFO FilterMutectCalls - Requester pays: disabled
23:44:52.890 INFO FilterMutectCalls - Initializing engine
23:44:53.088 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.NG6PoaAekz/LS0906.mutect2.raw.vcf.gz
23:44:53.199 INFO FilterMutectCalls - Done initializing engine
23:44:53.255 INFO ProgressMeter - Starting traversal
23:44:53.255 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:44:53.256 INFO FilterMutectCalls - Starting pass 0 through the variants
23:44:54.595 INFO FilterMutectCalls - Finished pass 0 through the variants
23:44:57.353 INFO FilterMutectCalls - Starting pass 1 through the variants
23:44:58.877 INFO FilterMutectCalls - Finished pass 1 through the variants
23:44:59.493 INFO FilterMutectCalls - Starting pass 2 through the variants
23:45:01.004 INFO FilterMutectCalls - Finished pass 2 through the variants
23:45:01.006 INFO FilterMutectCalls - Starting pass 3 through the variants
23:45:02.337 INFO FilterMutectCalls - Finished pass 3 through the variants
23:45:02.347 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:45:02.348 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:45:02.348 INFO ProgressMeter - chr6:29942827 0.2 9696 63978.9
23:45:02.348 INFO ProgressMeter - Traversal complete. Processed 9696 total variants in 0.2 minutes.
23:45:02.361 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:45:02 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 LS0906.mutect2.raw.vcf.gz --stats LS0906.mutect2.raw.vcf.gz.stats -O LS0906.mutect2.filtered.vcf.gz
23:45:03.507 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
23:45:03.593 INFO SelectVariants - ------------------------------------------------------------
23:45:03.595 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:45:03.595 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:45:03.595 INFO SelectVariants - Executing as ?@nf-4303c72a5dcb245e61eedf73e583d348-4a883-2tvxx on Linux v6.12.88 amd64
23:45:03.595 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:45:03.596 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:45:03 PM GMT
23:45:03.596 INFO SelectVariants - ------------------------------------------------------------
23:45:03.596 INFO SelectVariants - ------------------------------------------------------------
23:45:03.596 INFO SelectVariants - HTSJDK Version: 4.1.0
23:45:03.596 INFO SelectVariants - Picard Version: 3.1.1
23:45:03.597 INFO SelectVariants - Built for Spark Version: 3.5.0
23:45:03.597 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:45:03.597 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:45:03.597 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:45:03.597 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:45:03.597 INFO SelectVariants - Deflater: IntelDeflater
23:45:03.597 INFO SelectVariants - Inflater: IntelInflater
23:45:03.597 INFO SelectVariants - GCS max retries/reopens: 20
23:45:03.597 INFO SelectVariants - Requester pays: disabled
23:45:03.598 INFO SelectVariants - Initializing engine
23:45:03.707 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.NG6PoaAekz/LS0906.mutect2.filtered.vcf.gz
23:45:03.803 INFO SelectVariants - Done initializing engine
23:45:03.839 INFO ProgressMeter - Starting traversal
23:45:03.839 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:45:03.911 INFO ProgressMeter - chr7:13952561 0.0 2424 2077714.3
23:45:03.911 INFO ProgressMeter - Traversal complete. Processed 2424 total variants in 0.0 minutes.
23:45:03.922 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:45:03 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0906.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0906.mutect2.pass.vcf.gz