Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/11/04d7d1d835718bee6336bad0183a0d/.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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0891/LS0891_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/af-only-gnomad.hg38.vcf.gz.tbi
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0891/LS0891_tumor.bam.bai
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/11/04d7d1d835718bee6336bad0183a0d/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:38.585 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
22:44:38.694 INFO Mutect2 - ------------------------------------------------------------
22:44:38.697 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:38.697 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:38.697 INFO Mutect2 - Executing as ?@nf-1104d7d1d835718bee6336bad0183a0d-f475a-v95bx on Linux v6.12.88 amd64
22:44:38.697 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:38.697 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:38 PM GMT
22:44:38.697 INFO Mutect2 - ------------------------------------------------------------
22:44:38.697 INFO Mutect2 - ------------------------------------------------------------
22:44:38.698 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:38.698 INFO Mutect2 - Picard Version: 3.1.1
22:44:38.698 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:38.698 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:38.698 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:38.699 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:38.699 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:38.699 INFO Mutect2 - Deflater: IntelDeflater
22:44:38.699 INFO Mutect2 - Inflater: IntelInflater
22:44:38.699 INFO Mutect2 - GCS max retries/reopens: 20
22:44:38.699 INFO Mutect2 - Requester pays: disabled
22:44:38.699 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.CMBiRx36zZ/LS0891_tumor.bam.bai is older than BAM /tmp/nxf.CMBiRx36zZ/LS0891_tumor.bam
22:44:38.867 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.CMBiRx36zZ/af-only-gnomad.hg38.vcf.gz
22:44:38.985 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.CMBiRx36zZ/TST500C_manifest.bed
22:44:39.019 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:39.048 INFO Mutect2 - Done initializing engine
22:44:39.058 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
22:44:39.060 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
22:44:39.061 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:39.061 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:39.071 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
22:44:39.080 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:39.080 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:39.081 INFO IntelPairHmm - Available threads: 384
22:44:39.081 INFO IntelPairHmm - Requested threads: 4
22:44:39.081 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:39.124 INFO ProgressMeter - Starting traversal
22:44:39.125 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:50.175 INFO ProgressMeter - chr1:9721759 0.2 50 271.5
22:45:00.481 INFO ProgressMeter - chr1:11167440 0.4 110 309.1
22:45:11.442 INFO ProgressMeter - chr1:15909319 0.5 160 297.1
22:45:22.915 INFO ProgressMeter - chr1:15932804 0.7 200 274.0
22:45:33.893 INFO ProgressMeter - chr1:17018879 0.9 240 262.9
22:45:46.218 INFO ProgressMeter - chr1:18746718 1.1 290 259.3
22:45:57.061 INFO ProgressMeter - chr1:26763271 1.3 340 261.8
22:46:07.379 INFO ProgressMeter - chr1:36358356 1.5 380 258.3
22:46:18.616 INFO ProgressMeter - chr1:39899001 1.7 440 265.4
22:46:29.652 INFO ProgressMeter - chr1:45332211 1.8 500 271.4
22:46:40.383 INFO ProgressMeter - chr1:58780927 2.0 570 282.0
22:46:50.635 INFO ProgressMeter - chr1:77962768 2.2 640 292.0
22:47:01.292 INFO ProgressMeter - chr1:117210822 2.4 720 303.9
22:47:12.584 INFO ProgressMeter - chr1:119916198 2.6 760 297.1
22:47:23.425 INFO ProgressMeter - chr1:149852953 2.7 820 299.5
22:47:36.684 INFO ProgressMeter - chr1:156872825 3.0 860 290.6
22:47:47.658 INFO ProgressMeter - chr1:158620168 3.1 900 286.4
22:47:58.612 INFO ProgressMeter - chr1:158672057 3.3 960 288.7
22:48:08.901 INFO ProgressMeter - chr1:175988286 3.5 1020 291.7
22:48:19.978 INFO ProgressMeter - chr1:194909198 3.7 1090 296.1
22:48:31.880 INFO ProgressMeter - chr1:204518648 3.9 1150 296.5
22:48:41.902 INFO ProgressMeter - chr1:206478158 4.0 1210 299.0
22:48:52.196 INFO ProgressMeter - chr1:238275935 4.2 1280 303.5
22:49:04.925 INFO ProgressMeter - chr1:243503474 4.4 1330 300.2
22:49:15.685 INFO ProgressMeter - chr10:17151286 4.6 1380 299.4
22:49:26.077 INFO ProgressMeter - chr10:27063967 4.8 1430 299.0
22:49:37.449 INFO ProgressMeter - chr10:32031071 5.0 1490 299.7
22:49:47.674 INFO ProgressMeter - chr10:43112826 5.1 1540 299.5
22:49:58.570 INFO ProgressMeter - chr10:43117058 5.3 1570 294.9
22:50:08.988 INFO ProgressMeter - chr10:62057115 5.5 1620 294.7
22:50:20.398 INFO ProgressMeter - chr10:68645257 5.7 1660 291.8
22:50:31.505 INFO ProgressMeter - chr10:87894023 5.9 1720 292.9
22:50:43.261 INFO ProgressMeter - chr10:101770136 6.1 1790 294.9
22:50:53.268 INFO ProgressMeter - chr10:102597138 6.2 1850 296.7
22:51:05.566 INFO ProgressMeter - chr10:110601001 6.4 1900 295.0
22:51:16.660 INFO ProgressMeter - chr10:121480736 6.6 1960 295.8
22:51:27.380 INFO ProgressMeter - chr10:121485506 6.8 1990 292.5
22:51:38.639 INFO ProgressMeter - chr10:130900132 7.0 2040 291.8
22:51:49.018 INFO ProgressMeter - chr11:32434888 7.2 2110 294.5
22:51:59.111 INFO ProgressMeter - chr11:67434419 7.3 2180 297.3
22:52:10.038 INFO ProgressMeter - chr11:69698636 7.5 2240 298.1
22:52:20.759 INFO ProgressMeter - chr11:69708777 7.7 2280 296.3
22:52:37.855 INFO ProgressMeter - chr11:69811742 8.0 2340 293.3
22:52:48.022 INFO ProgressMeter - chr11:76458181 8.1 2380 292.1
22:52:59.291 INFO ProgressMeter - chr11:77344159 8.3 2440 292.7
22:53:12.119 INFO ProgressMeter - chr11:77420651 8.5 2480 290.1
22:53:22.938 INFO ProgressMeter - chr11:101062530 8.7 2550 292.1
22:53:38.451 INFO ProgressMeter - chr11:102328895 9.0 2590 288.1
22:53:49.638 INFO ProgressMeter - chr11:108329019 9.2 2660 289.9
22:54:00.793 INFO ProgressMeter - chr11:118473626 9.4 2710 289.5
22:54:11.440 INFO ProgressMeter - chr11:118503109 9.5 2760 289.4
22:54:22.371 INFO ProgressMeter - chr11:119206477 9.7 2800 288.0
22:54:32.704 INFO ProgressMeter - chr11:125626249 9.9 2830 286.1
22:54:43.546 INFO ProgressMeter - chr11:128458963 10.1 2890 286.9
22:54:57.101 INFO ProgressMeter - chr11:128460890 10.3 2910 282.5
22:55:07.181 INFO ProgressMeter - chr11:128781961 10.5 2960 282.8
22:55:17.494 INFO ProgressMeter - chr12:307971 10.6 3000 282.0
22:55:28.992 INFO ProgressMeter - chr12:4372829 10.8 3070 283.4
22:55:40.559 INFO ProgressMeter - chr12:4439592 11.0 3130 283.9
22:55:51.864 INFO ProgressMeter - chr12:6591464 11.2 3180 283.6
22:56:03.197 INFO ProgressMeter - chr12:11853593 11.4 3230 283.3
22:56:15.895 INFO ProgressMeter - chr12:11858738 11.6 3270 281.6
22:56:28.129 INFO ProgressMeter - chr12:11862961 11.8 3310 280.1
22:56:41.685 INFO ProgressMeter - chr12:11868383 12.0 3350 278.2
22:56:52.741 INFO ProgressMeter - chr12:25209243 12.2 3420 279.7
22:57:03.713 INFO ProgressMeter - chr12:31797567 12.4 3480 280.4
22:57:14.951 INFO ProgressMeter - chr12:45892009 12.6 3530 280.2
22:57:27.585 INFO ProgressMeter - chr12:49033175 12.8 3580 279.5
22:57:39.255 INFO ProgressMeter - chr12:49041441 13.0 3620 278.4
22:57:50.022 INFO ProgressMeter - chr12:49052925 13.2 3670 278.4
22:58:00.934 INFO ProgressMeter - chr12:56088019 13.4 3740 279.9
22:58:11.304 INFO ProgressMeter - chr12:57092975 13.5 3790 280.0
22:58:22.386 INFO ProgressMeter - chr12:57471675 13.7 3840 279.9
22:58:32.850 INFO ProgressMeter - chr12:68821705 13.9 3910 281.4
22:58:44.902 INFO ProgressMeter - chr12:92145386 14.1 3960 280.9
22:58:55.400 INFO ProgressMeter - chr12:114676311 14.3 4020 281.7
22:59:05.638 INFO ProgressMeter - chr12:132632431 14.4 4070 281.8
22:59:16.363 INFO ProgressMeter - chr12:132675396 14.6 4130 282.5
22:59:28.877 INFO ProgressMeter - chr13:21672392 14.8 4180 281.9
22:59:40.060 INFO ProgressMeter - chr13:28004050 15.0 4250 283.0
22:59:57.583 INFO ProgressMeter - chr13:28386232 15.3 4310 281.6
23:00:07.597 INFO ProgressMeter - chr13:28396958 15.5 4340 280.5
23:00:18.559 INFO ProgressMeter - chr13:32337583 15.7 4390 280.4
23:00:30.072 INFO ProgressMeter - chr13:32379364 15.8 4440 280.1
23:00:40.702 INFO ProgressMeter - chr13:48465203 16.0 4510 281.4
23:00:51.235 INFO ProgressMeter - chr13:102181777 16.2 4580 282.7
23:01:01.689 INFO ProgressMeter - chr13:102875690 16.4 4630 282.7
23:01:12.300 INFO ProgressMeter - chr13:113307937 16.6 4690 283.3
23:01:23.818 INFO ProgressMeter - chr14:35402830 16.7 4740 283.1
23:01:35.382 INFO ProgressMeter - chr14:37592575 16.9 4800 283.4
23:01:47.103 INFO ProgressMeter - chr14:65077410 17.1 4850 283.1
23:01:59.481 INFO ProgressMeter - chr14:95096038 17.3 4910 283.2
23:02:09.668 INFO ProgressMeter - chr14:102083544 17.5 4960 283.3
23:02:22.442 INFO ProgressMeter - chr15:34346419 17.7 5020 283.3
23:02:33.310 INFO ProgressMeter - chr15:34355662 17.9 5050 282.1
23:02:45.753 INFO ProgressMeter - chr15:41711139 18.1 5100 281.6
23:02:57.913 INFO ProgressMeter - chr15:41766019 18.3 5150 281.2
23:03:07.978 INFO ProgressMeter - chr15:53324680 18.5 5210 281.9
23:03:20.030 INFO ProgressMeter - chr15:87977592 18.7 5270 282.1
23:03:31.365 INFO ProgressMeter - chr15:89273375 18.9 5320 281.9
23:03:41.463 INFO ProgressMeter - chr15:90749639 19.0 5380 282.6
23:03:51.530 INFO ProgressMeter - chr15:92942841 19.2 5430 282.7
23:04:02.588 INFO ProgressMeter - chr15:98899593 19.4 5490 283.1
23:04:13.076 INFO ProgressMeter - chr16:346227 19.6 5540 283.1
23:04:23.686 INFO ProgressMeter - chr16:2086330 19.7 5600 283.6
23:04:34.770 INFO ProgressMeter - chr16:3590747 19.9 5680 285.0
23:04:46.611 INFO ProgressMeter - chr16:3728751 20.1 5720 284.2
23:04:57.218 INFO ProgressMeter - chr16:3810602 20.3 5780 284.7
23:05:08.998 INFO ProgressMeter - chr16:10180329 20.5 5830 284.4
23:05:21.454 INFO ProgressMeter - chr16:23637848 20.7 5890 284.5
23:05:32.611 INFO ProgressMeter - chr16:56821547 20.9 5950 284.8
23:05:43.232 INFO ProgressMeter - chr16:68811682 21.1 6010 285.3
23:05:54.670 INFO ProgressMeter - chr16:72794202 21.3 6050 284.6
23:06:06.071 INFO ProgressMeter - chr16:72798280 21.4 6080 283.5
23:06:16.948 INFO ProgressMeter - chr16:80072422 21.6 6120 282.9
23:06:27.600 INFO ProgressMeter - chr16:89279916 21.8 6180 283.4
23:06:40.008 INFO ProgressMeter - chr16:89285648 22.0 6220 282.5
23:06:50.899 INFO ProgressMeter - chr16:89815949 22.2 6290 283.4
23:07:03.547 INFO ProgressMeter - chr17:7676192 22.4 6350 283.4
23:07:13.911 INFO ProgressMeter - chr17:8206748 22.6 6410 283.9
23:07:26.017 INFO ProgressMeter - chr17:16101496 22.8 6480 284.4
23:07:36.685 INFO ProgressMeter - chr17:31201035 23.0 6550 285.3
23:07:47.149 INFO ProgressMeter - chr17:31350181 23.1 6610 285.7
23:07:58.087 INFO ProgressMeter - chr17:39470883 23.3 6680 286.5
23:08:08.461 INFO ProgressMeter - chr17:39715284 23.5 6740 286.9
23:08:18.681 INFO ProgressMeter - chr17:40398771 23.7 6800 287.4
23:08:29.941 INFO ProgressMeter - chr17:42307400 23.8 6880 288.5
23:08:40.519 INFO ProgressMeter - chr17:43086706 24.0 6950 289.3
23:08:51.971 INFO ProgressMeter - chr17:43112678 24.2 6990 288.7
23:09:02.306 INFO ProgressMeter - chr17:43533185 24.4 7030 288.3
23:09:14.082 INFO ProgressMeter - chr17:43540407 24.6 7080 288.0
23:09:26.123 INFO ProgressMeter - chr17:43544123 24.8 7110 286.9
23:09:36.963 INFO ProgressMeter - chr17:49601863 25.0 7170 287.2
23:09:48.421 INFO ProgressMeter - chr17:59902825 25.2 7230 287.4
23:09:59.037 INFO ProgressMeter - chr17:60633851 25.3 7290 287.8
23:10:09.402 INFO ProgressMeter - chr17:61857056 25.5 7340 287.8
23:10:20.569 INFO ProgressMeter - chr17:68529997 25.7 7400 288.0
23:10:31.131 INFO ProgressMeter - chr17:80923488 25.9 7470 288.8
23:10:42.455 INFO ProgressMeter - chr18:41990457 26.1 7540 289.4
23:10:54.023 INFO ProgressMeter - chr18:44951784 26.2 7590 289.2
23:11:04.140 INFO ProgressMeter - chr18:58671642 26.4 7640 289.2
23:11:14.558 INFO ProgressMeter - chr19:1621836 26.6 7710 290.0
23:11:25.398 INFO ProgressMeter - chr19:4054116 26.8 7790 291.0
23:11:36.732 INFO ProgressMeter - chr19:5245774 27.0 7860 291.5
23:11:48.084 INFO ProgressMeter - chr19:10140044 27.1 7930 292.1
23:11:58.738 INFO ProgressMeter - chr19:10985271 27.3 7990 292.4
23:12:09.707 INFO ProgressMeter - chr19:14516087 27.5 8060 293.0
23:12:20.477 INFO ProgressMeter - chr19:15179023 27.7 8110 292.9
23:12:32.066 INFO ProgressMeter - chr19:15254206 27.9 8170 293.0
23:12:42.642 INFO ProgressMeter - chr19:19147708 28.1 8250 294.0
23:12:53.717 INFO ProgressMeter - chr19:29823366 28.2 8310 294.2
23:13:04.167 INFO ProgressMeter - chr19:35729002 28.4 8370 294.5
23:13:15.318 INFO ProgressMeter - chr19:40246868 28.6 8430 294.7
23:13:26.102 INFO ProgressMeter - chr19:41252844 28.8 8490 295.0
23:13:36.345 INFO ProgressMeter - chr19:42289289 29.0 8530 294.6
23:13:46.531 INFO ProgressMeter - chr19:45353765 29.1 8580 294.6
23:13:57.674 INFO ProgressMeter - chr19:45413221 29.3 8650 295.1
23:14:09.065 INFO ProgressMeter - chr19:50406180 29.5 8710 295.3
23:14:20.660 INFO ProgressMeter - chr2:15940559 29.7 8760 295.0
23:14:31.503 INFO ProgressMeter - chr2:15950395 29.9 8810 294.9
23:14:43.305 INFO ProgressMeter - chr2:25248096 30.1 8870 295.0
23:14:56.024 INFO ProgressMeter - chr2:25753532 30.3 8920 294.6
23:15:09.736 INFO ProgressMeter - chr2:29224280 30.5 8970 294.0
23:15:21.164 INFO ProgressMeter - chr2:29275400 30.7 9000 293.2
23:15:32.651 INFO ProgressMeter - chr2:42295379 30.9 9060 293.3
23:15:44.006 INFO ProgressMeter - chr2:47410269 31.1 9110 293.1
23:15:54.550 INFO ProgressMeter - chr2:47790997 31.3 9140 292.4
23:16:05.748 INFO ProgressMeter - chr2:60921932 31.4 9200 292.6
23:16:16.901 INFO ProgressMeter - chr2:96254831 31.6 9240 292.1
23:16:30.761 INFO ProgressMeter - chr2:108763983 31.9 9320 292.5
23:16:42.132 INFO ProgressMeter - chr2:111126157 32.1 9370 292.4
23:16:54.215 INFO ProgressMeter - chr2:111128856 32.3 9390 291.1
23:17:07.639 INFO ProgressMeter - chr2:113223523 32.5 9430 290.4
23:17:19.694 INFO ProgressMeter - chr2:113226215 32.7 9450 289.2
23:17:32.809 INFO ProgressMeter - chr2:113229135 32.9 9480 288.2
23:17:44.475 INFO ProgressMeter - chr2:113232647 33.1 9510 287.4
23:17:56.475 INFO ProgressMeter - chr2:113234667 33.3 9530 286.3
23:18:08.255 INFO ProgressMeter - chr2:127289692 33.5 9580 286.1
23:18:18.448 INFO ProgressMeter - chr2:140475136 33.7 9640 286.4
23:18:29.304 INFO ProgressMeter - chr2:140850203 33.8 9700 286.7
23:18:39.917 INFO ProgressMeter - chr2:157765919 34.0 9750 286.7
23:18:51.779 INFO ProgressMeter - chr2:189864029 34.2 9810 286.8
23:19:02.794 INFO ProgressMeter - chr2:197409846 34.4 9880 287.3
23:19:14.586 INFO ProgressMeter - chr2:211386851 34.6 9940 287.4
23:19:25.217 INFO ProgressMeter - chr2:214781213 34.8 10000 287.6
23:19:38.539 INFO ProgressMeter - chr2:222201867 35.0 10040 286.9
23:19:51.237 INFO ProgressMeter - chr2:222207239 35.2 10080 286.3
23:20:01.404 INFO ProgressMeter - chr2:222211512 35.4 10110 285.8
23:20:13.663 INFO ProgressMeter - chr2:222216396 35.6 10150 285.3
23:20:26.068 INFO ProgressMeter - chr2:222220108 35.8 10180 284.5
23:20:38.563 INFO ProgressMeter - chr2:226796191 36.0 10240 284.5
23:20:50.321 INFO ProgressMeter - chr20:9565891 36.2 10290 284.4
23:21:01.479 INFO ProgressMeter - chr20:32434682 36.4 10340 284.3
23:21:12.422 INFO ProgressMeter - chr20:32800833 36.6 10390 284.2
23:21:24.064 INFO ProgressMeter - chr20:42110448 36.7 10460 284.6
23:21:34.144 INFO ProgressMeter - chr20:47635889 36.9 10510 284.7
23:21:46.076 INFO ProgressMeter - chr20:53576893 37.1 10540 284.0
23:21:56.168 INFO ProgressMeter - chr20:58854136 37.3 10580 283.8
23:22:08.266 INFO ProgressMeter - chr21:38380026 37.5 10650 284.1
23:22:19.326 INFO ProgressMeter - chr21:38423519 37.7 10690 283.8
23:22:29.969 INFO ProgressMeter - chr21:41473323 37.8 10730 283.5
23:22:47.846 INFO ProgressMeter - chr21:41491440 38.1 10760 282.1
23:23:00.254 INFO ProgressMeter - chr21:41499447 38.4 10790 281.3
23:23:10.891 INFO ProgressMeter - chr21:41503156 38.5 10820 280.8
23:23:20.992 INFO ProgressMeter - chr21:41506265 38.7 10850 280.4
23:23:32.052 INFO ProgressMeter - chr22:20983025 38.9 10900 280.3
23:23:44.521 INFO ProgressMeter - chr22:23290785 39.1 10970 280.6
23:23:55.804 INFO ProgressMeter - chr22:28701068 39.3 11020 280.6
23:24:06.773 INFO ProgressMeter - chr22:29284144 39.5 11090 281.0
23:24:17.709 INFO ProgressMeter - chr22:29299232 39.6 11130 280.8
23:24:28.294 INFO ProgressMeter - chr22:37974069 39.8 11170 280.5
23:24:39.367 INFO ProgressMeter - chr22:41177065 40.0 11230 280.7
23:24:50.031 INFO ProgressMeter - chr3:10072869 40.2 11290 281.0
23:25:00.945 INFO ProgressMeter - chr3:12353304 40.4 11340 280.9
23:25:13.307 INFO ProgressMeter - chr3:12357417 40.6 11370 280.3
23:25:27.237 INFO ProgressMeter - chr3:12361440 40.8 11400 279.4
23:25:38.957 INFO ProgressMeter - chr3:12366989 41.0 11440 279.0
23:25:51.335 INFO ProgressMeter - chr3:12372777 41.2 11480 278.6
23:26:03.294 INFO ProgressMeter - chr3:12378427 41.4 11520 278.2
23:26:13.555 INFO ProgressMeter - chr3:12606199 41.6 11570 278.3
23:26:24.398 INFO ProgressMeter - chr3:37012009 41.8 11630 278.5
23:26:35.177 INFO ProgressMeter - chr3:47084004 41.9 11690 278.8
23:26:46.574 INFO ProgressMeter - chr3:47124274 42.1 11740 278.7
23:26:58.266 INFO ProgressMeter - chr3:49896538 42.3 11800 278.8
23:27:08.562 INFO ProgressMeter - chr3:52564104 42.5 11860 279.1
23:27:18.822 INFO ProgressMeter - chr3:70965888 42.7 11920 279.4
23:27:29.886 INFO ProgressMeter - chr3:89341989 42.8 11990 279.8
23:27:41.246 INFO ProgressMeter - chr3:135106505 43.0 12050 280.0
23:27:52.202 INFO ProgressMeter - chr3:136422931 43.2 12100 280.0
23:28:03.877 INFO ProgressMeter - chr3:138737705 43.4 12160 280.1
23:28:14.343 INFO ProgressMeter - chr3:142524002 43.6 12220 280.4
23:28:25.836 INFO ProgressMeter - chr3:170293381 43.8 12280 280.5
23:28:36.520 INFO ProgressMeter - chr3:179232507 44.0 12340 280.7
23:28:48.906 INFO ProgressMeter - chr3:185472973 44.2 12400 280.8
23:29:00.409 INFO ProgressMeter - chr3:186048450 44.4 12430 280.2
23:29:11.416 INFO ProgressMeter - chr3:189789799 44.5 12490 280.4
23:29:22.518 INFO ProgressMeter - chr3:196066931 44.7 12550 280.6
23:29:32.729 INFO ProgressMeter - chr4:1805909 44.9 12620 281.1
23:29:44.125 INFO ProgressMeter - chr4:24541912 45.1 12690 281.5
23:29:54.607 INFO ProgressMeter - chr4:54267550 45.3 12750 281.7
23:30:06.269 INFO ProgressMeter - chr4:54699673 45.5 12810 281.8
23:30:17.190 INFO ProgressMeter - chr4:54733150 45.6 12840 281.4
23:30:28.687 INFO ProgressMeter - chr4:65367355 45.8 12900 281.5
23:30:39.921 INFO ProgressMeter - chr4:80281144 46.0 12960 281.7
23:30:52.323 INFO ProgressMeter - chr4:105236459 46.2 13020 281.7
23:31:03.008 INFO ProgressMeter - chr4:105242856 46.4 13060 281.5
23:31:13.265 INFO ProgressMeter - chr4:122876319 46.6 13120 281.7
23:31:23.432 INFO ProgressMeter - chr4:152352604 46.7 13190 282.2
23:31:33.716 INFO ProgressMeter - chr4:186603474 46.9 13240 282.2
23:31:44.009 INFO ProgressMeter - chr4:186619753 47.1 13280 282.1
23:31:55.386 INFO ProgressMeter - chr4:186708381 47.3 13320 281.8
23:32:05.503 INFO ProgressMeter - chr5:35856976 47.4 13370 281.8
23:32:15.982 INFO ProgressMeter - chr5:38981865 47.6 13430 282.1
23:32:27.118 INFO ProgressMeter - chr5:56871908 47.8 13500 282.4
23:32:37.186 INFO ProgressMeter - chr5:58459839 48.0 13550 282.5
23:32:47.524 INFO ProgressMeter - chr5:87268873 48.1 13620 282.9
23:32:57.608 INFO ProgressMeter - chr5:112838333 48.3 13680 283.2
23:33:09.739 INFO ProgressMeter - chr5:122391133 48.5 13720 282.8
23:33:20.387 INFO ProgressMeter - chr5:132609281 48.7 13770 282.8
23:33:31.537 INFO ProgressMeter - chr5:142630853 48.9 13830 283.0
23:33:42.947 INFO ProgressMeter - chr5:149511773 49.1 13870 282.7
23:33:54.566 INFO ProgressMeter - chr5:150124248 49.3 13930 282.8
23:34:05.443 INFO ProgressMeter - chr5:150402482 49.4 13980 282.8
23:34:16.594 INFO ProgressMeter - chr5:177085819 49.6 14040 282.9
23:34:27.046 INFO ProgressMeter - chr5:177092498 49.8 14070 282.5
23:34:38.567 INFO ProgressMeter - chr5:177209827 50.0 14110 282.3
23:34:48.695 INFO ProgressMeter - chr5:177280609 50.2 14150 282.1
23:34:59.048 INFO ProgressMeter - chr5:177516267 50.3 14200 282.1
23:35:10.265 INFO ProgressMeter - chr6:12059696 50.5 14260 282.3
23:35:21.473 INFO ProgressMeter - chr6:20484051 50.7 14330 282.6
23:35:31.700 INFO ProgressMeter - chr6:27810072 50.9 14400 283.0
23:35:43.240 INFO ProgressMeter - chr6:30705089 51.1 14440 282.8
23:35:54.316 INFO ProgressMeter - chr6:32202074 51.3 14490 282.7
23:36:05.219 INFO ProgressMeter - chr6:33320842 51.4 14540 282.7
23:36:15.522 INFO ProgressMeter - chr6:41964123 51.6 14610 283.1
23:36:25.599 INFO ProgressMeter - chr6:93245389 51.8 14680 283.5
23:36:36.295 INFO ProgressMeter - chr6:106106932 52.0 14740 283.7
23:36:46.852 INFO ProgressMeter - chr6:117318960 52.1 14790 283.7
23:36:58.612 INFO ProgressMeter - chr6:117323344 52.3 14820 283.2
23:37:09.264 INFO ProgressMeter - chr6:117328415 52.5 14860 283.0
23:37:22.474 INFO ProgressMeter - chr6:117334690 52.7 14900 282.6
23:37:33.556 INFO ProgressMeter - chr6:117340765 52.9 14940 282.4
23:37:44.369 INFO ProgressMeter - chr6:135190237 53.1 15000 282.6
23:37:55.251 INFO ProgressMeter - chr6:135205584 53.3 15030 282.2
23:38:07.027 INFO ProgressMeter - chr6:135210351 53.5 15070 281.9
23:38:20.933 INFO ProgressMeter - chr6:135212613 53.7 15090 281.0
23:38:33.315 INFO ProgressMeter - chr6:135216799 53.9 15130 280.7
23:38:43.923 INFO ProgressMeter - chr6:137881204 54.1 15180 280.7
23:38:55.682 INFO ProgressMeter - chr6:151700495 54.3 15230 280.6
23:39:05.780 INFO ProgressMeter - chr6:156777928 54.4 15280 280.7
23:39:17.505 INFO ProgressMeter - chr6:157206165 54.6 15330 280.6
23:39:27.758 INFO ProgressMeter - chr6:161098305 54.8 15370 280.4
23:39:38.198 INFO ProgressMeter - chr7:2922632 55.0 15440 280.8
23:39:49.997 INFO ProgressMeter - chr7:13892939 55.2 15510 281.1
23:40:01.823 INFO ProgressMeter - chr7:13908855 55.4 15550 280.8
23:40:12.153 INFO ProgressMeter - chr7:13932532 55.6 15570 280.3
23:40:23.869 INFO ProgressMeter - chr7:13938107 55.7 15610 280.0
23:40:34.977 INFO ProgressMeter - chr7:13944211 55.9 15650 279.8
23:40:45.857 INFO ProgressMeter - chr7:13947844 56.1 15680 279.4
23:40:58.619 INFO ProgressMeter - chr7:13950802 56.3 15700 278.7
23:41:11.340 INFO ProgressMeter - chr7:13955050 56.5 15730 278.2
23:41:23.788 INFO ProgressMeter - chr7:13960007 56.7 15770 277.9
23:41:36.227 INFO ProgressMeter - chr7:13963443 57.0 15800 277.4
23:41:48.834 INFO ProgressMeter - chr7:13969660 57.2 15840 277.1
23:41:59.387 INFO ProgressMeter - chr7:13973790 57.3 15870 276.8
23:42:11.030 INFO ProgressMeter - chr7:13976577 57.5 15890 276.2
23:42:23.098 INFO ProgressMeter - chr7:13981129 57.7 15930 275.9
23:42:38.419 INFO ProgressMeter - chr7:13984980 58.0 15960 275.2
23:42:49.060 INFO ProgressMeter - chr7:13988792 58.2 15980 274.7
23:43:02.205 INFO ProgressMeter - chr7:55153138 58.4 16040 274.7
23:43:13.034 INFO ProgressMeter - chr7:55166876 58.6 16080 274.6
23:43:24.629 INFO ProgressMeter - chr7:55170497 58.8 16110 274.2
23:43:35.044 INFO ProgressMeter - chr7:55178190 58.9 16150 274.0
23:43:47.350 INFO ProgressMeter - chr7:55200541 59.1 16190 273.8
23:43:57.609 INFO ProgressMeter - chr7:78369154 59.3 16240 273.8
23:44:08.947 INFO ProgressMeter - chr7:86839709 59.5 16300 274.0
23:44:19.992 INFO ProgressMeter - chr7:102189792 59.7 16370 274.3
23:44:30.134 INFO ProgressMeter - chr7:106868078 59.9 16420 274.4
23:44:41.378 INFO ProgressMeter - chr7:116759335 60.0 16470 274.3
23:44:51.741 INFO ProgressMeter - chr7:129212079 60.2 16520 274.4
23:45:02.538 INFO ProgressMeter - chr7:140790027 60.4 16560 274.2
23:45:13.977 INFO ProgressMeter - chr7:140849003 60.6 16610 274.2
23:45:24.179 INFO ProgressMeter - chr7:148817875 60.8 16680 274.6
23:45:36.228 INFO ProgressMeter - chr7:152163810 61.0 16740 274.6
23:45:48.190 INFO ProgressMeter - chr7:152182972 61.2 16780 274.4
23:45:59.549 INFO ProgressMeter - chr7:152649321 61.3 16850 274.7
23:46:10.385 INFO ProgressMeter - chr8:32083130 61.5 16920 275.0
23:46:20.833 INFO ProgressMeter - chr8:32742673 61.7 16970 275.1
23:46:32.799 INFO ProgressMeter - chr8:37834046 61.9 17030 275.1
23:46:43.587 INFO ProgressMeter - chr8:38431079 62.1 17090 275.3
23:46:53.603 INFO ProgressMeter - chr8:41934478 62.2 17130 275.2
23:47:04.657 INFO ProgressMeter - chr8:47798282 62.4 17190 275.4
23:47:15.817 INFO ProgressMeter - chr8:47902621 62.6 17250 275.5
23:47:27.448 INFO ProgressMeter - chr8:56010096 62.8 17330 275.9
23:47:38.412 INFO ProgressMeter - chr8:75606427 63.0 17400 276.2
23:47:50.517 INFO ProgressMeter - chr8:116863128 63.2 17470 276.5
23:48:02.713 INFO ProgressMeter - chr8:127740446 63.4 17520 276.4
23:48:13.212 INFO ProgressMeter - chr9:5003244 63.6 17590 276.7
23:48:23.604 INFO ProgressMeter - chr9:5534743 63.7 17650 276.9
23:48:34.091 INFO ProgressMeter - chr9:8504259 63.9 17700 276.9
23:48:45.011 INFO ProgressMeter - chr9:20622243 64.1 17740 276.8
23:48:55.222 INFO ProgressMeter - chr9:35078731 64.3 17790 276.8
23:49:07.758 INFO ProgressMeter - chr9:84670791 64.5 17850 276.8
23:49:18.497 INFO ProgressMeter - chr9:84743784 64.7 17870 276.4
23:49:30.592 INFO ProgressMeter - chr9:84812834 64.9 17900 276.0
23:49:47.322 INFO ProgressMeter - chr9:84861364 65.1 17930 275.3
23:50:00.874 INFO ProgressMeter - chr9:84864822 65.4 17960 274.8
23:50:11.566 INFO ProgressMeter - chr9:84874179 65.5 17990 274.5
23:50:25.441 INFO ProgressMeter - chr9:85022183 65.8 18030 274.1
23:50:39.580 INFO ProgressMeter - chr9:85026401 66.0 18060 273.6
23:50:52.235 INFO ProgressMeter - chr9:95467290 66.2 18120 273.6
23:51:02.764 INFO ProgressMeter - chr9:107485749 66.4 18170 273.7
23:51:15.151 INFO ProgressMeter - chr9:130884955 66.6 18230 273.7
23:51:26.612 INFO ProgressMeter - chr9:132906087 66.8 18270 273.5
23:51:37.401 INFO ProgressMeter - chr9:136505478 67.0 18320 273.6
23:51:48.335 INFO ProgressMeter - chr9:136923875 67.2 18390 273.9
23:51:59.384 INFO ProgressMeter - chrX:40072528 67.3 18450 274.0
23:52:11.253 INFO ProgressMeter - chrX:45076695 67.5 18500 273.9
23:52:23.607 INFO ProgressMeter - chrX:47180273 67.7 18530 273.5
23:52:33.709 INFO ProgressMeter - chrX:48793791 67.9 18580 273.6
23:52:49.167 INFO ProgressMeter - chrX:49035140 68.2 18610 273.0
23:53:01.262 INFO ProgressMeter - chrX:49038606 68.4 18640 272.6
23:53:12.905 INFO ProgressMeter - chrX:53214738 68.6 18690 272.6
23:53:24.462 INFO ProgressMeter - chrX:53409400 68.8 18740 272.6
23:53:36.845 INFO ProgressMeter - chrX:64192612 69.0 18780 272.3
23:53:47.862 INFO ProgressMeter - chrX:67569185 69.1 18810 272.0
23:53:57.884 INFO ProgressMeter - chrX:71121738 69.3 18860 272.1
23:54:09.245 INFO ProgressMeter - chrX:71137724 69.5 18920 272.2
23:54:20.520 INFO ProgressMeter - chrX:71406636 69.7 18960 272.1
23:54:31.496 INFO ProgressMeter - chrX:77676224 69.9 19020 272.2
23:54:41.916 INFO ProgressMeter - chrX:101356782 70.0 19060 272.1
23:54:52.772 INFO ProgressMeter - chrX:124037525 70.2 19120 272.3
23:55:03.140 INFO ProgressMeter - chrX:130013332 70.4 19180 272.4
23:55:14.164 INFO ProgressMeter - chrX:134377990 70.6 19220 272.3
23:55:16.985 INFO Mutect2 - 850137 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
11 read(s) filtered by: ReadLengthReadFilter
169 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
850317 total reads filtered out of 122506578 reads processed
23:55:16.985 INFO ProgressMeter - chrY:20489365 70.6 19274 272.9
23:55:16.985 INFO ProgressMeter - Traversal complete. Processed 19274 total regions in 70.6 minutes.
23:55:17.001 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 8.254088609
23:55:17.001 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 379.846532094
23:55:17.001 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.69 sec
23:55:17.002 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:55:17 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 70.64 minutes.
Runtime.totalMemory()=4194304000
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 LS0891_tumor.bam --tumor-sample LS0891 -L TST500C_manifest.bed -O LS0891.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:55:18.511 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
23:55:18.623 INFO FilterMutectCalls - ------------------------------------------------------------
23:55:18.625 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:55:18.625 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:55:18.625 INFO FilterMutectCalls - Executing as ?@nf-1104d7d1d835718bee6336bad0183a0d-f475a-v95bx on Linux v6.12.88 amd64
23:55:18.625 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:55:18.625 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:55:18 PM GMT
23:55:18.626 INFO FilterMutectCalls - ------------------------------------------------------------
23:55:18.626 INFO FilterMutectCalls - ------------------------------------------------------------
23:55:18.626 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:55:18.627 INFO FilterMutectCalls - Picard Version: 3.1.1
23:55:18.627 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:55:18.627 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:55:18.627 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:55:18.627 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:55:18.627 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:55:18.627 INFO FilterMutectCalls - Deflater: IntelDeflater
23:55:18.627 INFO FilterMutectCalls - Inflater: IntelInflater
23:55:18.628 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:55:18.628 INFO FilterMutectCalls - Requester pays: disabled
23:55:18.628 INFO FilterMutectCalls - Initializing engine
23:55:18.799 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.CMBiRx36zZ/LS0891.mutect2.raw.vcf.gz
23:55:18.918 INFO FilterMutectCalls - Done initializing engine
23:55:18.968 INFO ProgressMeter - Starting traversal
23:55:18.968 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:55:18.969 INFO FilterMutectCalls - Starting pass 0 through the variants
23:55:20.838 INFO FilterMutectCalls - Finished pass 0 through the variants
23:55:22.898 INFO FilterMutectCalls - Starting pass 1 through the variants
23:55:24.821 INFO FilterMutectCalls - Finished pass 1 through the variants
23:55:25.492 INFO FilterMutectCalls - Starting pass 2 through the variants
23:55:27.362 INFO FilterMutectCalls - Finished pass 2 through the variants
23:55:27.365 INFO FilterMutectCalls - Starting pass 3 through the variants
23:55:28.927 INFO FilterMutectCalls - Finished pass 3 through the variants
23:55:28.934 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:55:28.935 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:55:28.935 INFO ProgressMeter - chr7:13952608 0.2 11580 69710.0
23:55:28.935 INFO ProgressMeter - Traversal complete. Processed 11580 total variants in 0.2 minutes.
23:55:28.945 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:55:28 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=620756992
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 LS0891.mutect2.raw.vcf.gz --stats LS0891.mutect2.raw.vcf.gz.stats -O LS0891.mutect2.filtered.vcf.gz
23:55:30.203 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
23:55:30.307 INFO SelectVariants - ------------------------------------------------------------
23:55:30.309 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:55:30.309 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:55:30.310 INFO SelectVariants - Executing as ?@nf-1104d7d1d835718bee6336bad0183a0d-f475a-v95bx on Linux v6.12.88 amd64
23:55:30.310 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:55:30.310 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:55:30 PM GMT
23:55:30.310 INFO SelectVariants - ------------------------------------------------------------
23:55:30.310 INFO SelectVariants - ------------------------------------------------------------
23:55:30.310 INFO SelectVariants - HTSJDK Version: 4.1.0
23:55:30.310 INFO SelectVariants - Picard Version: 3.1.1
23:55:30.310 INFO SelectVariants - Built for Spark Version: 3.5.0
23:55:30.310 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:55:30.311 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:55:30.311 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:55:30.311 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:55:30.311 INFO SelectVariants - Deflater: IntelDeflater
23:55:30.311 INFO SelectVariants - Inflater: IntelInflater
23:55:30.311 INFO SelectVariants - GCS max retries/reopens: 20
23:55:30.311 INFO SelectVariants - Requester pays: disabled
23:55:30.311 INFO SelectVariants - Initializing engine
23:55:30.476 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.CMBiRx36zZ/LS0891.mutect2.filtered.vcf.gz
23:55:30.576 INFO SelectVariants - Done initializing engine
23:55:30.611 INFO ProgressMeter - Starting traversal
23:55:30.611 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:55:30.684 INFO ProgressMeter - chr6:20489473 0.0 2895 2481428.6
23:55:30.684 INFO ProgressMeter - Traversal complete. Processed 2895 total variants in 0.0 minutes.
23:55:30.694 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:55:30 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=335544320
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 LS0891.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0891.mutect2.pass.vcf.gz