Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/13/619acb8bedbd3445dc346fad0710fa/.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/13/619acb8bedbd3445dc346fad0710fa/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0890/LS0890_tumor.bam
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0890/LS0890_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:37.035 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
22:44:37.154 INFO Mutect2 - ------------------------------------------------------------
22:44:37.156 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:37.157 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:37.157 INFO Mutect2 - Executing as ?@nf-13619acb8bedbd3445dc346fad0710fa-d5fe4-bccmm on Linux v6.12.88 amd64
22:44:37.157 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:37.157 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:36 PM GMT
22:44:37.157 INFO Mutect2 - ------------------------------------------------------------
22:44:37.157 INFO Mutect2 - ------------------------------------------------------------
22:44:37.158 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:37.158 INFO Mutect2 - Picard Version: 3.1.1
22:44:37.159 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:37.159 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:37.159 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:37.159 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:37.159 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:37.159 INFO Mutect2 - Deflater: IntelDeflater
22:44:37.159 INFO Mutect2 - Inflater: IntelInflater
22:44:37.159 INFO Mutect2 - GCS max retries/reopens: 20
22:44:37.160 INFO Mutect2 - Requester pays: disabled
22:44:37.160 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.hpKFKkGGGr/LS0890_tumor.bam.bai is older than BAM /tmp/nxf.hpKFKkGGGr/LS0890_tumor.bam
22:44:37.328 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.hpKFKkGGGr/af-only-gnomad.hg38.vcf.gz
22:44:37.446 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.hpKFKkGGGr/TST500C_manifest.bed
22:44:37.481 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:37.508 INFO Mutect2 - Done initializing engine
22:44:37.518 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
22:44:37.519 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
22:44:37.520 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:37.520 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:37.530 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
22:44:37.539 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:37.539 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:37.539 INFO IntelPairHmm - Available threads: 384
22:44:37.539 INFO IntelPairHmm - Requested threads: 4
22:44:37.539 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:37.575 INFO ProgressMeter - Starting traversal
22:44:37.576 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:47.603 INFO ProgressMeter - chr1:9715548 0.2 30 179.5
22:44:59.002 INFO ProgressMeter - chr1:11127047 0.4 80 224.0
22:45:11.212 INFO ProgressMeter - chr1:11231298 0.6 120 214.1
22:45:23.335 INFO ProgressMeter - chr1:15919402 0.8 160 209.8
22:45:35.352 INFO ProgressMeter - chr1:15932058 1.0 190 197.3
22:45:48.360 INFO ProgressMeter - chr1:15937810 1.2 220 186.5
22:45:58.403 INFO ProgressMeter - chr1:18745112 1.3 260 193.0
22:46:09.607 INFO ProgressMeter - chr1:23557510 1.5 290 189.1
22:46:20.332 INFO ProgressMeter - chr1:26773800 1.7 340 198.5
22:46:30.496 INFO ProgressMeter - chr1:36467228 1.9 380 201.9
22:46:41.080 INFO ProgressMeter - chr1:39897679 2.1 430 208.9
22:46:52.331 INFO ProgressMeter - chr1:43348946 2.2 480 213.7
22:47:03.797 INFO ProgressMeter - chr1:46270657 2.4 540 221.6
22:47:14.485 INFO ProgressMeter - chr1:64844062 2.6 600 229.4
22:47:25.565 INFO ProgressMeter - chr1:85267625 2.8 660 235.7
22:47:38.354 INFO ProgressMeter - chr1:117623596 3.0 730 242.3
22:47:50.357 INFO ProgressMeter - chr1:119922332 3.2 770 239.7
22:48:00.504 INFO ProgressMeter - chr1:119968075 3.4 810 239.5
22:48:17.509 INFO ProgressMeter - chr1:156873119 3.7 860 234.6
22:48:27.996 INFO ProgressMeter - chr1:158611262 3.8 890 231.8
22:48:39.829 INFO ProgressMeter - chr1:158657475 4.0 950 235.3
22:48:50.484 INFO ProgressMeter - chr1:162778654 4.2 1000 237.2
22:49:01.259 INFO ProgressMeter - chr1:179126524 4.4 1060 241.2
22:49:12.615 INFO ProgressMeter - chr1:204457726 4.6 1130 246.5
22:49:22.690 INFO ProgressMeter - chr1:204542549 4.8 1180 248.3
22:49:32.895 INFO ProgressMeter - chr1:206768634 4.9 1230 249.9
22:49:43.845 INFO ProgressMeter - chr1:239718564 5.1 1290 252.7
22:49:58.625 INFO ProgressMeter - chr1:243501667 5.4 1320 246.7
22:50:10.890 INFO ProgressMeter - chr1:243545508 5.6 1350 243.0
22:50:21.886 INFO ProgressMeter - chr10:27035461 5.7 1400 244.0
22:50:33.635 INFO ProgressMeter - chr10:32009950 5.9 1450 244.3
22:50:45.319 INFO ProgressMeter - chr10:43105093 6.1 1510 246.4
22:50:55.856 INFO ProgressMeter - chr10:43114574 6.3 1540 244.3
22:51:06.555 INFO ProgressMeter - chr10:43117806 6.5 1570 242.2
22:51:18.187 INFO ProgressMeter - chr10:62091325 6.7 1620 242.6
22:51:28.534 INFO ProgressMeter - chr10:68645856 6.8 1650 240.9
22:51:40.447 INFO ProgressMeter - chr10:87914240 7.0 1700 241.2
22:51:50.609 INFO ProgressMeter - chr10:101769329 7.2 1750 242.5
22:52:01.428 INFO ProgressMeter - chr10:101779590 7.4 1790 242.0
22:52:13.915 INFO ProgressMeter - chr10:110590970 7.6 1840 241.9
22:52:25.190 INFO ProgressMeter - chr10:113158665 7.8 1880 241.2
22:52:37.248 INFO ProgressMeter - chr10:121481758 8.0 1910 238.9
22:52:48.480 INFO ProgressMeter - chr10:121529344 8.2 1950 238.3
22:53:00.307 INFO ProgressMeter - chr11:17719874 8.4 2010 239.9
22:53:11.684 INFO ProgressMeter - chr11:64368472 8.6 2070 241.6
22:53:22.914 INFO ProgressMeter - chr11:69643830 8.8 2130 243.3
22:53:33.961 INFO ProgressMeter - chr11:69700007 8.9 2180 243.9
22:53:45.141 INFO ProgressMeter - chr11:69769888 9.1 2220 243.3
22:53:58.329 INFO ProgressMeter - chr11:69779115 9.3 2260 241.8
22:54:08.946 INFO ProgressMeter - chr11:69813032 9.5 2280 239.4
22:54:19.628 INFO ProgressMeter - chr11:76472681 9.7 2320 239.2
22:54:32.904 INFO ProgressMeter - chr11:77353534 9.9 2370 238.9
22:54:43.555 INFO ProgressMeter - chr11:86268454 10.1 2430 240.6
22:54:55.340 INFO ProgressMeter - chr11:102114246 10.3 2490 241.8
22:55:06.633 INFO ProgressMeter - chr11:108227623 10.5 2520 240.4
22:55:17.659 INFO ProgressMeter - chr11:108317445 10.7 2580 241.8
22:55:31.084 INFO ProgressMeter - chr11:118473839 10.9 2640 242.4
22:55:43.941 INFO ProgressMeter - chr11:118503830 11.1 2690 242.2
22:55:55.268 INFO ProgressMeter - chr11:119278508 11.3 2730 241.7
22:56:06.937 INFO ProgressMeter - chr11:125634534 11.5 2760 240.2
22:56:18.268 INFO ProgressMeter - chr11:128459450 11.7 2810 240.6
22:56:29.977 INFO ProgressMeter - chr11:128463507 11.9 2830 238.3
22:56:43.509 INFO ProgressMeter - chr11:128812603 12.1 2880 238.0
22:56:54.062 INFO ProgressMeter - chr12:333485 12.3 2920 237.9
22:57:05.514 INFO ProgressMeter - chr12:4372592 12.5 2980 239.1
22:57:16.623 INFO ProgressMeter - chr12:4438023 12.7 3030 239.5
22:57:28.701 INFO ProgressMeter - chr12:6582846 12.9 3080 239.6
22:57:40.500 INFO ProgressMeter - chr12:11752429 13.0 3120 239.1
22:57:52.195 INFO ProgressMeter - chr12:11856948 13.2 3150 237.8
22:58:05.146 INFO ProgressMeter - chr12:11861389 13.5 3190 237.0
22:58:17.394 INFO ProgressMeter - chr12:11864939 13.7 3220 235.7
22:58:33.026 INFO ProgressMeter - chr12:11869732 13.9 3250 233.4
22:58:43.616 INFO ProgressMeter - chr12:18562813 14.1 3310 234.7
22:58:53.900 INFO ProgressMeter - chr12:31791757 14.3 3370 236.1
22:59:05.377 INFO ProgressMeter - chr12:45851162 14.5 3400 235.1
22:59:17.397 INFO ProgressMeter - chr12:49029059 14.7 3450 235.3
22:59:30.221 INFO ProgressMeter - chr12:49034065 14.9 3480 233.9
22:59:40.909 INFO ProgressMeter - chr12:49040932 15.1 3510 233.1
22:59:51.360 INFO ProgressMeter - chr12:49051215 15.2 3550 233.1
23:00:01.473 INFO ProgressMeter - chr12:51980967 15.4 3600 233.8
23:00:13.277 INFO ProgressMeter - chr12:56101059 15.6 3660 234.7
23:00:27.082 INFO ProgressMeter - chr12:57095032 15.8 3700 233.8
23:00:38.343 INFO ProgressMeter - chr12:57750303 16.0 3750 234.2
23:00:50.664 INFO ProgressMeter - chr12:68836913 16.2 3810 234.9
23:01:00.888 INFO ProgressMeter - chr12:111418800 16.4 3860 235.5
23:01:11.414 INFO ProgressMeter - chr12:114682943 16.6 3910 236.1
23:01:22.775 INFO ProgressMeter - chr12:132639123 16.8 3960 236.4
23:01:33.977 INFO ProgressMeter - chr12:132675396 16.9 4010 236.7
23:01:45.023 INFO ProgressMeter - chr13:20989209 17.1 4050 236.5
23:01:56.486 INFO ProgressMeter - chr13:21703931 17.3 4100 236.8
23:02:07.264 INFO ProgressMeter - chr13:28308887 17.5 4160 237.8
23:02:20.265 INFO ProgressMeter - chr13:28386002 17.7 4190 236.6
23:02:33.347 INFO ProgressMeter - chr13:28399042 17.9 4230 235.9
23:02:47.066 INFO ProgressMeter - chr13:32338531 18.2 4280 235.7
23:02:58.844 INFO ProgressMeter - chr13:32389375 18.4 4330 235.9
23:03:09.033 INFO ProgressMeter - chr13:72761361 18.5 4390 237.0
23:03:19.984 INFO ProgressMeter - chr13:102181777 18.7 4450 237.9
23:03:31.554 INFO ProgressMeter - chr13:106285972 18.9 4500 238.1
23:03:42.829 INFO ProgressMeter - chr13:113304127 19.1 4550 238.4
23:03:54.740 INFO ProgressMeter - chr14:23183020 19.3 4590 238.0
23:04:06.279 INFO ProgressMeter - chr14:37588189 19.5 4640 238.2
23:04:16.675 INFO ProgressMeter - chr14:37596657 19.7 4690 238.7
23:04:27.403 INFO ProgressMeter - chr14:68497450 19.8 4740 239.0
23:04:39.524 INFO ProgressMeter - chr14:95103417 20.0 4790 239.1
23:04:49.925 INFO ProgressMeter - chr14:102085896 20.2 4840 239.5
23:05:01.229 INFO ProgressMeter - chr15:34346257 20.4 4890 239.8
23:05:12.715 INFO ProgressMeter - chr15:34355890 20.6 4920 239.0
23:05:23.251 INFO ProgressMeter - chr15:41697000 20.8 4960 238.9
23:05:35.028 INFO ProgressMeter - chr15:41749688 21.0 5000 238.6
23:05:46.582 INFO ProgressMeter - chr15:49430215 21.2 5050 238.8
23:05:56.903 INFO ProgressMeter - chr15:67181239 21.3 5110 239.7
23:06:09.540 INFO ProgressMeter - chr15:88032855 21.5 5160 239.6
23:06:20.174 INFO ProgressMeter - chr15:89301324 21.7 5220 240.4
23:06:30.926 INFO ProgressMeter - chr15:90763149 21.9 5270 240.8
23:06:41.825 INFO ProgressMeter - chr15:92992857 22.1 5330 241.5
23:06:53.868 INFO ProgressMeter - chr15:98916775 22.3 5380 241.6
23:07:04.815 INFO ProgressMeter - chr16:2060668 22.5 5430 241.8
23:07:15.972 INFO ProgressMeter - chr16:2175109 22.6 5490 242.5
23:07:27.219 INFO ProgressMeter - chr16:3595603 22.8 5550 243.1
23:07:38.088 INFO ProgressMeter - chr16:3731832 23.0 5580 242.5
23:07:48.414 INFO ProgressMeter - chr16:9763202 23.2 5630 242.9
23:07:58.965 INFO ProgressMeter - chr16:11254841 23.4 5670 242.8
23:08:11.388 INFO ProgressMeter - chr16:23635988 23.6 5720 242.7
23:08:23.131 INFO ProgressMeter - chr16:56805502 23.8 5780 243.3
23:08:34.610 INFO ProgressMeter - chr16:68801668 24.0 5840 243.8
23:08:46.788 INFO ProgressMeter - chr16:72793738 24.2 5880 243.4
23:08:59.908 INFO ProgressMeter - chr16:72797784 24.4 5910 242.5
23:09:10.378 INFO ProgressMeter - chr16:72959860 24.5 5940 242.0
23:09:21.780 INFO ProgressMeter - chr16:89268476 24.7 6000 242.6
23:09:35.009 INFO ProgressMeter - chr16:89283270 25.0 6040 242.0
23:09:46.188 INFO ProgressMeter - chr16:89773269 25.1 6090 242.2
23:09:57.649 INFO ProgressMeter - chr17:7671854 25.3 6150 242.8
23:10:08.084 INFO ProgressMeter - chr17:7679765 25.5 6190 242.7
23:10:18.830 INFO ProgressMeter - chr17:12141145 25.7 6260 243.7
23:10:29.947 INFO ProgressMeter - chr17:16101733 25.9 6310 243.9
23:10:41.361 INFO ProgressMeter - chr17:31206238 26.1 6380 244.8
23:10:52.702 INFO ProgressMeter - chr17:31356565 26.3 6440 245.3
23:11:04.626 INFO ProgressMeter - chr17:39492749 26.5 6500 245.7
23:11:15.374 INFO ProgressMeter - chr17:39715865 26.6 6550 246.0
23:11:26.524 INFO ProgressMeter - chr17:40389963 26.8 6600 246.1
23:11:38.055 INFO ProgressMeter - chr17:42291970 27.0 6670 247.0
23:11:49.061 INFO ProgressMeter - chr17:43052248 27.2 6730 247.5
23:12:01.572 INFO ProgressMeter - chr17:43093183 27.4 6780 247.4
23:12:13.107 INFO ProgressMeter - chr17:43528462 27.6 6820 247.2
23:12:26.728 INFO ProgressMeter - chr17:43534272 27.8 6850 246.2
23:12:38.466 INFO ProgressMeter - chr17:43539718 28.0 6890 245.9
23:12:51.425 INFO ProgressMeter - chr17:43543955 28.2 6920 245.1
23:13:03.217 INFO ProgressMeter - chr17:48726788 28.4 6960 244.8
23:13:14.610 INFO ProgressMeter - chr17:58709857 28.6 7010 245.0
23:13:24.962 INFO ProgressMeter - chr17:59936213 28.8 7070 245.6
23:13:36.427 INFO ProgressMeter - chr17:61715949 29.0 7110 245.3
23:13:48.334 INFO ProgressMeter - chr17:65538245 29.2 7160 245.4
23:13:58.391 INFO ProgressMeter - chr17:76737055 29.3 7210 245.7
23:14:09.602 INFO ProgressMeter - chr18:745843 29.5 7270 246.2
23:14:22.374 INFO ProgressMeter - chr18:44949994 29.7 7340 246.8
23:14:33.135 INFO ProgressMeter - chr18:45063664 29.9 7370 246.3
23:14:43.331 INFO ProgressMeter - chr18:59893269 30.1 7430 246.9
23:14:54.374 INFO ProgressMeter - chr19:1650175 30.3 7490 247.4
23:15:05.306 INFO ProgressMeter - chr19:3119204 30.5 7550 247.8
23:15:16.546 INFO ProgressMeter - chr19:5216718 30.6 7610 248.3
23:15:26.779 INFO ProgressMeter - chr19:7128850 30.8 7660 248.5
23:15:37.068 INFO ProgressMeter - chr19:10148882 31.0 7710 248.8
23:15:49.371 INFO ProgressMeter - chr19:10986477 31.2 7770 249.1
23:15:59.786 INFO ProgressMeter - chr19:12940051 31.4 7830 249.6
23:16:11.620 INFO ProgressMeter - chr19:15170329 31.6 7870 249.3
23:16:23.355 INFO ProgressMeter - chr19:15200786 31.8 7920 249.3
23:16:33.754 INFO ProgressMeter - chr19:17832923 31.9 7970 249.6
23:16:43.931 INFO ProgressMeter - chr19:27972374 32.1 8030 250.1
23:16:54.728 INFO ProgressMeter - chr19:29823988 32.3 8080 250.3
23:17:06.410 INFO ProgressMeter - chr19:35730340 32.5 8140 250.6
23:17:16.554 INFO ProgressMeter - chr19:40240511 32.6 8190 250.8
23:17:28.512 INFO ProgressMeter - chr19:41259551 32.8 8250 251.1
23:17:40.175 INFO ProgressMeter - chr19:41880668 33.0 8270 250.3
23:17:51.145 INFO ProgressMeter - chr19:45351699 33.2 8320 250.4
23:18:01.374 INFO ProgressMeter - chr19:45371871 33.4 8380 250.9
23:18:12.264 INFO ProgressMeter - chr19:47228156 33.6 8440 251.4
23:18:22.736 INFO ProgressMeter - chr19:52225715 33.8 8500 251.8
23:18:33.478 INFO ProgressMeter - chr2:15943586 33.9 8530 251.4
23:18:44.986 INFO ProgressMeter - chr2:17781536 34.1 8580 251.4
23:18:55.170 INFO ProgressMeter - chr2:25300137 34.3 8630 251.7
23:19:07.228 INFO ProgressMeter - chr2:25767581 34.5 8670 251.3
23:19:18.122 INFO ProgressMeter - chr2:29222988 34.7 8710 251.2
23:19:29.345 INFO ProgressMeter - chr2:29225503 34.9 8730 250.4
23:19:39.370 INFO ProgressMeter - chr2:29320760 35.0 8760 250.1
23:19:49.902 INFO ProgressMeter - chr2:42282841 35.2 8800 250.0
23:20:01.242 INFO ProgressMeter - chr2:47403190 35.4 8850 250.0
23:20:12.160 INFO ProgressMeter - chr2:47790925 35.6 8880 249.6
23:20:22.232 INFO ProgressMeter - chr2:58163027 35.7 8920 249.6
23:20:38.346 INFO ProgressMeter - chr2:96253806 36.0 8980 249.4
23:20:48.836 INFO ProgressMeter - chr2:108751262 36.2 9040 249.8
23:20:59.684 INFO ProgressMeter - chr2:108773045 36.4 9090 249.9
23:21:14.997 INFO ProgressMeter - chr2:111127666 36.6 9120 249.0
23:21:26.719 INFO ProgressMeter - chr2:113221036 36.8 9150 248.5
23:21:41.550 INFO ProgressMeter - chr2:113224920 37.1 9180 247.7
23:21:55.066 INFO ProgressMeter - chr2:113227165 37.3 9200 246.7
23:22:06.444 INFO ProgressMeter - chr2:113231190 37.5 9230 246.3
23:22:22.093 INFO ProgressMeter - chr2:113233451 37.7 9250 245.1
23:22:32.741 INFO ProgressMeter - chr2:113236195 37.9 9280 244.7
23:22:44.732 INFO ProgressMeter - chr2:136115710 38.1 9330 244.8
23:22:55.006 INFO ProgressMeter - chr2:140516887 38.3 9390 245.2
23:23:06.927 INFO ProgressMeter - chr2:141049173 38.5 9450 245.5
23:23:17.213 INFO ProgressMeter - chr2:172592933 38.7 9500 245.7
23:23:28.140 INFO ProgressMeter - chr2:191064805 38.8 9560 246.1
23:23:39.027 INFO ProgressMeter - chr2:201272896 39.0 9620 246.5
23:23:49.197 INFO ProgressMeter - chr2:211665321 39.2 9670 246.7
23:23:59.814 INFO ProgressMeter - chr2:219574952 39.4 9720 246.9
23:24:12.433 INFO ProgressMeter - chr2:222203605 39.6 9750 246.3
23:24:22.555 INFO ProgressMeter - chr2:222206738 39.7 9780 246.0
23:24:34.641 INFO ProgressMeter - chr2:222211284 40.0 9820 245.8
23:24:45.205 INFO ProgressMeter - chr2:222215661 40.1 9850 245.5
23:24:58.360 INFO ProgressMeter - chr2:222218764 40.3 9870 244.6
23:25:09.006 INFO ProgressMeter - chr2:224497751 40.5 9910 244.5
23:25:19.213 INFO ProgressMeter - chr2:226796757 40.7 9950 244.5
23:25:31.805 INFO ProgressMeter - chr20:9644123 40.9 10000 244.5
23:25:44.100 INFO ProgressMeter - chr20:32436476 41.1 10050 244.5
23:25:54.435 INFO ProgressMeter - chr20:41029429 41.3 10110 244.9
23:26:05.697 INFO ProgressMeter - chr20:42472524 41.5 10170 245.2
23:26:17.356 INFO ProgressMeter - chr20:52679538 41.7 10220 245.3
23:26:28.947 INFO ProgressMeter - chr20:58840207 41.9 10260 245.1
23:26:40.714 INFO ProgressMeter - chr21:30000000 42.1 10320 245.4
23:26:50.792 INFO ProgressMeter - chr21:38381228 42.2 10350 245.1
23:27:01.722 INFO ProgressMeter - chr21:38400304 42.4 10380 244.8
23:27:12.999 INFO ProgressMeter - chr21:41465818 42.6 10420 244.7
23:27:23.948 INFO ProgressMeter - chr21:41490567 42.8 10450 244.3
23:27:35.515 INFO ProgressMeter - chr21:41491480 43.0 10460 243.5
23:27:47.045 INFO ProgressMeter - chr21:41498456 43.2 10490 243.1
23:27:59.571 INFO ProgressMeter - chr21:41502840 43.4 10530 242.8
23:28:11.457 INFO ProgressMeter - chr21:41506612 43.6 10560 242.4
23:28:23.477 INFO ProgressMeter - chr22:20983025 43.8 10610 242.4
23:28:34.806 INFO ProgressMeter - chr22:23288095 44.0 10670 242.8
23:28:46.437 INFO ProgressMeter - chr22:23291720 44.1 10690 242.1
23:28:56.639 INFO ProgressMeter - chr22:28706967 44.3 10740 242.3
23:29:09.699 INFO ProgressMeter - chr22:29284014 44.5 10810 242.7
23:29:20.159 INFO ProgressMeter - chr22:29286807 44.7 10830 242.2
23:29:30.362 INFO ProgressMeter - chr22:33163485 44.9 10870 242.2
23:29:41.062 INFO ProgressMeter - chr22:41176245 45.1 10920 242.4
23:29:51.742 INFO ProgressMeter - chr3:10047915 45.2 10960 242.3
23:30:02.241 INFO ProgressMeter - chr3:12352918 45.4 11010 242.5
23:30:15.127 INFO ProgressMeter - chr3:12357758 45.6 11040 242.0
23:30:27.664 INFO ProgressMeter - chr3:12360638 45.8 11060 241.3
23:30:38.053 INFO ProgressMeter - chr3:12365134 46.0 11090 241.0
23:30:48.623 INFO ProgressMeter - chr3:12369021 46.2 11120 240.8
23:31:00.312 INFO ProgressMeter - chr3:12373484 46.4 11150 240.4
23:31:14.527 INFO ProgressMeter - chr3:12376257 46.6 11170 239.6
23:31:26.229 INFO ProgressMeter - chr3:12591706 46.8 11210 239.5
23:31:36.778 INFO ProgressMeter - chr3:30644745 47.0 11260 239.6
23:31:48.647 INFO ProgressMeter - chr3:41225453 47.2 11330 240.1
23:31:58.697 INFO ProgressMeter - chr3:47103348 47.4 11380 240.3
23:32:09.885 INFO ProgressMeter - chr3:49396006 47.5 11420 240.2
23:32:19.923 INFO ProgressMeter - chr3:49895959 47.7 11470 240.4
23:32:31.371 INFO ProgressMeter - chr3:52561765 47.9 11520 240.5
23:32:42.516 INFO ProgressMeter - chr3:69964845 48.1 11580 240.8
23:32:54.073 INFO ProgressMeter - chr3:72842278 48.3 11640 241.1
23:33:04.959 INFO ProgressMeter - chr3:120002044 48.5 11690 241.2
23:33:16.877 INFO ProgressMeter - chr3:136341420 48.7 11740 241.3
23:33:27.154 INFO ProgressMeter - chr3:138692274 48.8 11790 241.5
23:33:38.227 INFO ProgressMeter - chr3:142485185 49.0 11850 241.8
23:33:49.408 INFO ProgressMeter - chr3:170259967 49.2 11910 242.1
23:33:59.612 INFO ProgressMeter - chr3:179220984 49.4 11970 242.5
23:34:10.043 INFO ProgressMeter - chr3:183527981 49.5 12020 242.6
23:34:21.498 INFO ProgressMeter - chr3:186047428 49.7 12060 242.5
23:34:32.868 INFO ProgressMeter - chr3:187729286 49.9 12110 242.6
23:34:42.906 INFO ProgressMeter - chr3:196058572 50.1 12160 242.8
23:34:53.085 INFO ProgressMeter - chr4:1803195 50.3 12220 243.1
23:35:03.853 INFO ProgressMeter - chr4:20595695 50.4 12280 243.5
23:35:14.563 INFO ProgressMeter - chr4:41750984 50.6 12330 243.6
23:35:25.217 INFO ProgressMeter - chr4:54295262 50.8 12380 243.7
23:35:41.534 INFO ProgressMeter - chr4:54737173 51.1 12430 243.4
23:35:51.657 INFO ProgressMeter - chr4:65348052 51.2 12480 243.6
23:36:03.432 INFO ProgressMeter - chr4:80285644 51.4 12540 243.8
23:36:14.039 INFO ProgressMeter - chr4:105235447 51.6 12590 244.0
23:36:24.563 INFO ProgressMeter - chr4:105241031 51.8 12630 243.9
23:36:37.877 INFO ProgressMeter - chr4:105276168 52.0 12660 243.4
23:36:49.307 INFO ProgressMeter - chr4:142208464 52.2 12730 243.9
23:37:01.885 INFO ProgressMeter - chr4:186596642 52.4 12790 244.1
23:37:15.508 INFO ProgressMeter - chr4:186619082 52.6 12840 244.0
23:37:27.946 INFO ProgressMeter - chr4:186706892 52.8 12880 243.8
23:37:38.727 INFO ProgressMeter - chr5:236426 53.0 12920 243.7
23:37:49.796 INFO ProgressMeter - chr5:38957650 53.2 12980 244.0
23:38:00.662 INFO ProgressMeter - chr5:44370662 53.4 13050 244.5
23:38:12.618 INFO ProgressMeter - chr5:58455283 53.6 13100 244.5
23:38:23.955 INFO ProgressMeter - chr5:80675033 53.8 13160 244.7
23:38:36.089 INFO ProgressMeter - chr5:112827195 54.0 13240 245.3
23:38:48.820 INFO ProgressMeter - chr5:112841669 54.2 13280 245.1
23:39:00.861 INFO ProgressMeter - chr5:122451252 54.4 13320 244.9
23:39:11.507 INFO ProgressMeter - chr5:138904412 54.6 13380 245.2
23:39:22.756 INFO ProgressMeter - chr5:142671822 54.8 13430 245.3
23:39:33.759 INFO ProgressMeter - chr5:150060860 54.9 13470 245.2
23:39:45.638 INFO ProgressMeter - chr5:150132843 55.1 13520 245.2
23:39:56.950 INFO ProgressMeter - chr5:150406258 55.3 13560 245.1
23:40:12.622 INFO ProgressMeter - chr5:177090936 55.6 13620 245.0
23:40:27.510 INFO ProgressMeter - chr5:177135947 55.8 13660 244.7
23:40:38.056 INFO ProgressMeter - chr5:177292088 56.0 13700 244.6
23:40:48.827 INFO ProgressMeter - chr5:180608980 56.2 13750 244.7
23:40:59.295 INFO ProgressMeter - chr6:398826 56.4 13800 244.8
23:41:10.171 INFO ProgressMeter - chr6:20472963 56.5 13860 245.1
23:41:20.263 INFO ProgressMeter - chr6:26049873 56.7 13910 245.3
23:41:35.472 INFO ProgressMeter - chr6:30700563 57.0 13960 245.1
23:41:47.898 INFO ProgressMeter - chr6:30712289 57.2 14000 244.9
23:41:58.168 INFO ProgressMeter - chr6:32212822 57.3 14050 245.0
23:42:10.529 INFO ProgressMeter - chr6:35455848 57.5 14100 245.0
23:42:21.117 INFO ProgressMeter - chr6:41968050 57.7 14160 245.3
23:42:32.826 INFO ProgressMeter - chr6:93358254 57.9 14230 245.7
23:42:43.098 INFO ProgressMeter - chr6:111702883 58.1 14280 245.8
23:42:53.957 INFO ProgressMeter - chr6:117319296 58.3 14320 245.7
23:43:04.079 INFO ProgressMeter - chr6:117322888 58.4 14340 245.4
23:43:17.006 INFO ProgressMeter - chr6:117328621 58.7 14380 245.2
23:43:28.754 INFO ProgressMeter - chr6:117333721 58.9 14420 245.0
23:43:39.717 INFO ProgressMeter - chr6:117340064 59.0 14460 244.9
23:43:50.952 INFO ProgressMeter - chr6:117394614 59.2 14510 245.0
23:44:05.299 INFO ProgressMeter - chr6:135206136 59.5 14560 244.9
23:44:15.676 INFO ProgressMeter - chr6:135208949 59.6 14580 244.5
23:44:29.129 INFO ProgressMeter - chr6:135213021 59.9 14610 244.1
23:44:42.942 INFO ProgressMeter - chr6:135217752 60.1 14640 243.6
23:44:55.368 INFO ProgressMeter - chr6:149679873 60.3 14680 243.5
23:45:06.342 INFO ProgressMeter - chr6:151366394 60.5 14710 243.2
23:45:17.238 INFO ProgressMeter - chr6:151944194 60.7 14750 243.2
23:45:28.030 INFO ProgressMeter - chr6:156778124 60.8 14780 242.9
23:45:41.669 INFO ProgressMeter - chr6:157206165 61.1 14830 242.8
23:45:52.796 INFO ProgressMeter - chr6:161091377 61.3 14870 242.8
23:46:03.925 INFO ProgressMeter - chr6:163561980 61.4 14920 242.8
23:46:15.358 INFO ProgressMeter - chr7:5977650 61.6 14970 242.9
23:46:29.149 INFO ProgressMeter - chr7:13894904 61.9 15020 242.8
23:46:46.349 INFO ProgressMeter - chr7:13931800 62.1 15050 242.2
23:46:58.337 INFO ProgressMeter - chr7:13935966 62.3 15080 241.9
23:47:11.033 INFO ProgressMeter - chr7:13942163 62.6 15120 241.7
23:47:22.661 INFO ProgressMeter - chr7:13945804 62.8 15150 241.4
23:47:37.285 INFO ProgressMeter - chr7:13950268 63.0 15180 241.0
23:47:50.648 INFO ProgressMeter - chr7:13952646 63.2 15200 240.4
23:48:03.011 INFO ProgressMeter - chr7:13955567 63.4 15220 240.0
23:48:14.501 INFO ProgressMeter - chr7:13960262 63.6 15250 239.7
23:48:27.609 INFO ProgressMeter - chr7:13963443 63.8 15270 239.2
23:48:39.579 INFO ProgressMeter - chr7:13967608 64.0 15300 238.9
23:48:49.930 INFO ProgressMeter - chr7:13971386 64.2 15330 238.8
23:49:02.096 INFO ProgressMeter - chr7:13975232 64.4 15360 238.5
23:49:19.991 INFO ProgressMeter - chr7:13978698 64.7 15380 237.7
23:49:31.074 INFO ProgressMeter - chr7:13982011 64.9 15410 237.5
23:49:41.101 INFO ProgressMeter - chr7:13984809 65.1 15430 237.2
23:49:52.759 INFO ProgressMeter - chr7:13988523 65.3 15450 236.8
23:50:04.618 INFO ProgressMeter - chr7:50399916 65.5 15490 236.7
23:50:14.791 INFO ProgressMeter - chr7:55153981 65.6 15520 236.5
23:50:25.873 INFO ProgressMeter - chr7:55166647 65.8 15550 236.3
23:50:38.627 INFO ProgressMeter - chr7:55170613 66.0 15580 236.0
23:50:50.742 INFO ProgressMeter - chr7:55177634 66.2 15610 235.7
23:51:04.990 INFO ProgressMeter - chr7:55181057 66.5 15640 235.3
23:51:15.897 INFO ProgressMeter - chr7:55205524 66.6 15670 235.1
23:51:27.204 INFO ProgressMeter - chr7:81717230 66.8 15720 235.2
23:51:40.195 INFO ProgressMeter - chr7:92686998 67.0 15770 235.2
23:51:52.013 INFO ProgressMeter - chr7:102201339 67.2 15830 235.4
23:52:04.420 INFO ProgressMeter - chr7:106868736 67.4 15880 235.4
23:52:14.808 INFO ProgressMeter - chr7:116757435 67.6 15920 235.4
23:52:26.239 INFO ProgressMeter - chr7:129211033 67.8 15970 235.5
23:52:36.934 INFO ProgressMeter - chr7:140790725 68.0 16020 235.6
23:52:48.283 INFO ProgressMeter - chr7:140847019 68.2 16060 235.6
23:53:00.152 INFO ProgressMeter - chr7:148828738 68.4 16130 235.9
23:53:10.779 INFO ProgressMeter - chr7:152162473 68.6 16180 236.0
23:53:23.156 INFO ProgressMeter - chr7:152181818 68.8 16220 235.9
23:53:34.832 INFO ProgressMeter - chr7:152648640 69.0 16280 236.1
23:53:44.880 INFO ProgressMeter - chr8:31640138 69.1 16340 236.4
23:53:55.069 INFO ProgressMeter - chr8:32647203 69.3 16380 236.4
23:54:07.858 INFO ProgressMeter - chr8:37695978 69.5 16420 236.2
23:54:19.121 INFO ProgressMeter - chr8:38413668 69.7 16470 236.3
23:54:31.156 INFO ProgressMeter - chr8:38452504 69.9 16510 236.2
23:54:44.614 INFO ProgressMeter - chr8:41934309 70.1 16540 235.9
23:54:56.068 INFO ProgressMeter - chr8:47776842 70.3 16580 235.8
23:55:08.990 INFO ProgressMeter - chr8:47852671 70.5 16630 235.8
23:55:19.872 INFO ProgressMeter - chr8:47929090 70.7 16680 235.9
23:55:31.002 INFO ProgressMeter - chr8:55999416 70.9 16730 236.0
23:55:42.639 INFO ProgressMeter - chr8:68134216 71.1 16780 236.1
23:55:53.526 INFO ProgressMeter - chr8:91970656 71.3 16830 236.2
23:56:04.831 INFO ProgressMeter - chr8:127731968 71.5 16870 236.1
23:56:15.277 INFO ProgressMeter - chr8:127738847 71.6 16900 235.9
23:56:26.079 INFO ProgressMeter - chr8:138386796 71.8 16930 235.8
23:56:37.152 INFO ProgressMeter - chr9:5024390 72.0 16980 235.9
23:56:48.522 INFO ProgressMeter - chr9:5126331 72.2 17020 235.8
23:56:59.433 INFO ProgressMeter - chr9:8486000 72.4 17070 235.9
23:57:13.185 INFO ProgressMeter - chr9:20622243 72.6 17120 235.8
23:57:25.822 INFO ProgressMeter - chr9:35078710 72.8 17160 235.7
23:57:36.405 INFO ProgressMeter - chr9:83971861 73.0 17200 235.7
23:57:51.266 INFO ProgressMeter - chr9:84742950 73.2 17240 235.4
23:58:04.672 INFO ProgressMeter - chr9:84812688 73.5 17270 235.1
23:58:20.559 INFO ProgressMeter - chr9:84861038 73.7 17290 234.5
23:58:36.653 INFO ProgressMeter - chr9:84864828 74.0 17320 234.1
23:58:48.543 INFO ProgressMeter - chr9:84873773 74.2 17350 233.9
23:59:00.038 INFO ProgressMeter - chr9:84955281 74.4 17380 233.7
23:59:10.049 INFO ProgressMeter - chr9:85024312 74.5 17400 233.4
23:59:20.908 INFO ProgressMeter - chr9:90874670 74.7 17430 233.3
23:59:32.713 INFO ProgressMeter - chr9:95468876 74.9 17480 233.3
23:59:43.321 INFO ProgressMeter - chr9:99144730 75.1 17520 233.3
23:59:55.883 INFO ProgressMeter - chr9:130874866 75.3 17570 233.3
00:00:07.145 INFO ProgressMeter - chr9:132896555 75.5 17600 233.1
00:00:18.638 INFO ProgressMeter - chr9:136497036 75.7 17640 233.1
00:00:29.072 INFO ProgressMeter - chr9:136511235 75.9 17680 233.1
00:00:39.756 INFO ProgressMeter - chr9:136920232 76.0 17730 233.2
00:00:52.643 INFO ProgressMeter - chrX:40073182 76.3 17800 233.4
00:01:03.769 INFO ProgressMeter - chrX:47181747 76.4 17870 233.8
00:01:14.064 INFO ProgressMeter - chrX:49034735 76.6 17930 234.0
00:01:24.255 INFO ProgressMeter - chrX:53196684 76.8 17990 234.3
00:01:35.164 INFO ProgressMeter - chrX:53413146 77.0 18050 234.5
00:01:47.757 INFO ProgressMeter - chrX:67545585 77.2 18090 234.4
00:01:58.541 INFO ProgressMeter - chrX:71121560 77.3 18150 234.6
00:02:09.985 INFO ProgressMeter - chrX:71366313 77.5 18210 234.8
00:02:20.510 INFO ProgressMeter - chrX:77557449 77.7 18270 235.1
00:02:30.816 INFO ProgressMeter - chrX:77693822 77.9 18320 235.2
00:02:41.455 INFO ProgressMeter - chrX:124061316 78.1 18400 235.7
00:02:52.344 INFO ProgressMeter - chrX:130024988 78.2 18450 235.8
00:03:03.131 INFO ProgressMeter - chrY:15839678 78.4 18510 236.0
00:03:06.668 INFO Mutect2 - 864081 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
225 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
864306 total reads filtered out of 149073698 reads processed
00:03:06.668 INFO ProgressMeter - chrY:20489416 78.5 18537 236.2
00:03:06.668 INFO ProgressMeter - Traversal complete. Processed 18537 total regions in 78.5 minutes.
00:03:06.686 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 9.010631522
00:03:06.686 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 400.562825302
00:03:06.686 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 14.66 sec
00:03:06.687 INFO Mutect2 - Shutting down engine
[June 9, 2026 at 12:03:06 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 78.49 minutes.
Runtime.totalMemory()=3221225472
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 LS0890_tumor.bam --tumor-sample LS0890 -L TST500C_manifest.bed -O LS0890.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
00:03:08.154 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
00:03:08.234 INFO FilterMutectCalls - ------------------------------------------------------------
00:03:08.241 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
00:03:08.241 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
00:03:08.241 INFO FilterMutectCalls - Executing as ?@nf-13619acb8bedbd3445dc346fad0710fa-d5fe4-bccmm on Linux v6.12.88 amd64
00:03:08.241 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
00:03:08.242 INFO FilterMutectCalls - Start Date/Time: June 9, 2026 at 12:03:08 AM GMT
00:03:08.242 INFO FilterMutectCalls - ------------------------------------------------------------
00:03:08.242 INFO FilterMutectCalls - ------------------------------------------------------------
00:03:08.243 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
00:03:08.243 INFO FilterMutectCalls - Picard Version: 3.1.1
00:03:08.243 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
00:03:08.243 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:03:08.243 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:03:08.243 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:03:08.243 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:03:08.244 INFO FilterMutectCalls - Deflater: IntelDeflater
00:03:08.244 INFO FilterMutectCalls - Inflater: IntelInflater
00:03:08.244 INFO FilterMutectCalls - GCS max retries/reopens: 20
00:03:08.244 INFO FilterMutectCalls - Requester pays: disabled
00:03:08.244 INFO FilterMutectCalls - Initializing engine
00:03:08.348 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.hpKFKkGGGr/LS0890.mutect2.raw.vcf.gz
00:03:08.443 INFO FilterMutectCalls - Done initializing engine
00:03:08.491 INFO ProgressMeter - Starting traversal
00:03:08.491 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
00:03:08.492 INFO FilterMutectCalls - Starting pass 0 through the variants
00:03:09.932 INFO FilterMutectCalls - Finished pass 0 through the variants
00:03:11.272 INFO FilterMutectCalls - Starting pass 1 through the variants
00:03:12.746 INFO FilterMutectCalls - Finished pass 1 through the variants
00:03:13.171 INFO FilterMutectCalls - Starting pass 2 through the variants
00:03:14.635 INFO FilterMutectCalls - Finished pass 2 through the variants
00:03:14.637 INFO FilterMutectCalls - Starting pass 3 through the variants
00:03:15.794 INFO FilterMutectCalls - Finished pass 3 through the variants
00:03:15.800 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
00:03:15.800 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
00:03:15.800 INFO ProgressMeter - chr6:41954899 0.1 10676 87639.9
00:03:15.800 INFO ProgressMeter - Traversal complete. Processed 10676 total variants in 0.1 minutes.
00:03:15.810 INFO FilterMutectCalls - Shutting down engine
[June 9, 2026 at 12:03:15 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=503316480
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0890.mutect2.raw.vcf.gz --stats LS0890.mutect2.raw.vcf.gz.stats -O LS0890.mutect2.filtered.vcf.gz
00:03:16.945 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
00:03:17.025 INFO SelectVariants - ------------------------------------------------------------
00:03:17.027 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
00:03:17.027 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
00:03:17.027 INFO SelectVariants - Executing as ?@nf-13619acb8bedbd3445dc346fad0710fa-d5fe4-bccmm on Linux v6.12.88 amd64
00:03:17.027 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
00:03:17.027 INFO SelectVariants - Start Date/Time: June 9, 2026 at 12:03:16 AM GMT
00:03:17.027 INFO SelectVariants - ------------------------------------------------------------
00:03:17.027 INFO SelectVariants - ------------------------------------------------------------
00:03:17.028 INFO SelectVariants - HTSJDK Version: 4.1.0
00:03:17.028 INFO SelectVariants - Picard Version: 3.1.1
00:03:17.028 INFO SelectVariants - Built for Spark Version: 3.5.0
00:03:17.028 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:03:17.028 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:03:17.028 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:03:17.028 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:03:17.028 INFO SelectVariants - Deflater: IntelDeflater
00:03:17.029 INFO SelectVariants - Inflater: IntelInflater
00:03:17.029 INFO SelectVariants - GCS max retries/reopens: 20
00:03:17.029 INFO SelectVariants - Requester pays: disabled
00:03:17.029 INFO SelectVariants - Initializing engine
00:03:17.132 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.hpKFKkGGGr/LS0890.mutect2.filtered.vcf.gz
00:03:17.224 INFO SelectVariants - Done initializing engine
00:03:17.257 INFO ProgressMeter - Starting traversal
00:03:17.257 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
00:03:17.324 INFO ProgressMeter - chr6:89084175 0.0 2669 2426363.6
00:03:17.325 INFO ProgressMeter - Traversal complete. Processed 2669 total variants in 0.0 minutes.
00:03:17.334 INFO SelectVariants - Shutting down engine
[June 9, 2026 at 12:03:17 AM 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 LS0890.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0890.mutect2.pass.vcf.gz