Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0923/LS0923_tumor.bam.bai
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0923/LS0923_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/c2/32a592e17e15d2e40c57697f4e52d7/.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/c2/32a592e17e15d2e40c57697f4e52d7/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:04.709 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
22:44:04.823 INFO Mutect2 - ------------------------------------------------------------
22:44:04.826 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:04.826 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:04.826 INFO Mutect2 - Executing as ?@nf-c232a592e17e15d2e40c57697f4e52d7-81a8e-wz48l on Linux v6.12.88 amd64
22:44:04.826 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:04.827 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:04 PM GMT
22:44:04.827 INFO Mutect2 - ------------------------------------------------------------
22:44:04.827 INFO Mutect2 - ------------------------------------------------------------
22:44:04.828 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:04.828 INFO Mutect2 - Picard Version: 3.1.1
22:44:04.828 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:04.828 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:04.828 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:04.828 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:04.829 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:04.829 INFO Mutect2 - Deflater: IntelDeflater
22:44:04.829 INFO Mutect2 - Inflater: IntelInflater
22:44:04.830 INFO Mutect2 - GCS max retries/reopens: 20
22:44:04.830 INFO Mutect2 - Requester pays: disabled
22:44:04.830 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.hCEJhDZ57F/LS0923_tumor.bam.bai is older than BAM /tmp/nxf.hCEJhDZ57F/LS0923_tumor.bam
22:44:04.972 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.hCEJhDZ57F/af-only-gnomad.hg38.vcf.gz
22:44:05.076 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.hCEJhDZ57F/TST500C_manifest.bed
22:44:05.107 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:05.131 INFO Mutect2 - Done initializing engine
22:44:05.139 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
22:44:05.140 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
22:44:05.141 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:05.141 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:05.150 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
22:44:05.158 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:05.158 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:05.158 INFO IntelPairHmm - Available threads: 384
22:44:05.158 INFO IntelPairHmm - Requested threads: 4
22:44:05.158 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:05.188 INFO ProgressMeter - Starting traversal
22:44:05.189 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:16.207 INFO ProgressMeter - chr1:11127622 0.2 60 326.8
22:44:26.491 INFO ProgressMeter - chr1:15876500 0.4 120 338.0
22:44:38.049 INFO ProgressMeter - chr1:17022606 0.5 170 310.4
22:44:48.169 INFO ProgressMeter - chr1:26697371 0.7 230 321.1
22:44:59.096 INFO ProgressMeter - chr1:36466355 0.9 280 311.7
22:45:09.627 INFO ProgressMeter - chr1:43339962 1.1 350 325.9
22:45:20.734 INFO ProgressMeter - chr1:58779729 1.3 430 341.5
22:45:30.819 INFO ProgressMeter - chr1:77969923 1.4 510 357.4
22:45:41.101 INFO ProgressMeter - chr1:117623814 1.6 580 362.8
22:45:52.822 INFO ProgressMeter - chr1:155904433 1.8 650 362.3
22:46:02.956 INFO ProgressMeter - chr1:156875080 2.0 680 346.4
22:46:13.207 INFO ProgressMeter - chr1:158661285 2.1 740 346.8
22:46:24.544 INFO ProgressMeter - chr1:179108353 2.3 820 353.1
22:46:35.338 INFO ProgressMeter - chr1:204525748 2.5 910 363.6
22:46:45.475 INFO ProgressMeter - chr1:226388654 2.7 1000 374.3
22:46:56.937 INFO ProgressMeter - chr1:243504118 2.9 1060 370.3
22:47:07.674 INFO ProgressMeter - chr10:27060324 3.0 1130 371.5
22:47:18.509 INFO ProgressMeter - chr10:43102402 3.2 1210 375.5
22:47:29.438 INFO ProgressMeter - chr10:43116087 3.4 1260 370.1
22:47:39.820 INFO ProgressMeter - chr10:62090860 3.6 1310 366.2
22:47:50.542 INFO ProgressMeter - chr10:87879949 3.8 1370 364.8
22:48:01.404 INFO ProgressMeter - chr10:101772301 3.9 1440 365.8
22:48:14.342 INFO ProgressMeter - chr10:110603163 4.2 1520 366.0
22:48:25.623 INFO ProgressMeter - chr10:121518680 4.3 1590 366.3
22:48:36.518 INFO ProgressMeter - chr11:64361467 4.5 1680 371.5
22:48:47.191 INFO ProgressMeter - chr11:69698533 4.7 1770 376.6
22:48:57.273 INFO ProgressMeter - chr11:69777079 4.9 1840 378.0
22:49:07.803 INFO ProgressMeter - chr11:69818712 5.0 1880 372.8
22:49:18.857 INFO ProgressMeter - chr11:77379239 5.2 1950 373.0
22:49:29.536 INFO ProgressMeter - chr11:101062745 5.4 2020 373.7
22:49:41.657 INFO ProgressMeter - chr11:108252885 5.6 2080 370.9
22:49:52.915 INFO ProgressMeter - chr11:108325308 5.8 2150 371.0
22:50:03.936 INFO ProgressMeter - chr11:118473585 6.0 2210 369.6
22:50:13.948 INFO ProgressMeter - chr11:118507527 6.1 2260 367.7
22:50:25.207 INFO ProgressMeter - chr11:125638675 6.3 2310 364.7
22:50:35.837 INFO ProgressMeter - chr11:128460588 6.5 2350 360.9
22:50:47.522 INFO ProgressMeter - chr12:297089 6.7 2410 359.4
22:50:57.926 INFO ProgressMeter - chr12:4375229 6.9 2490 362.0
22:51:08.202 INFO ProgressMeter - chr12:4450552 7.1 2550 361.7
22:51:18.594 INFO ProgressMeter - chr12:11752429 7.2 2600 359.9
22:51:30.785 INFO ProgressMeter - chr12:11860500 7.4 2650 356.8
22:51:44.606 INFO ProgressMeter - chr12:11868391 7.7 2700 352.6
22:51:55.046 INFO ProgressMeter - chr12:25221301 7.8 2780 355.0
22:52:05.289 INFO ProgressMeter - chr12:45851770 8.0 2840 354.9
22:52:16.360 INFO ProgressMeter - chr12:49033531 8.2 2890 353.0
22:52:26.506 INFO ProgressMeter - chr12:49050297 8.4 2940 351.9
22:52:36.506 INFO ProgressMeter - chr12:56085023 8.5 3000 352.0
22:52:48.155 INFO ProgressMeter - chr12:57463690 8.7 3070 352.2
22:52:58.383 INFO ProgressMeter - chr12:68820805 8.9 3150 354.5
22:53:08.796 INFO ProgressMeter - chr12:112450444 9.1 3230 356.5
22:53:18.806 INFO ProgressMeter - chr12:132639123 9.2 3300 357.6
22:53:29.471 INFO ProgressMeter - chr13:21045683 9.4 3370 358.3
22:53:40.356 INFO ProgressMeter - chr13:28035621 9.6 3450 359.9
22:53:51.914 INFO ProgressMeter - chr13:28388492 9.8 3510 358.9
22:54:02.124 INFO ProgressMeter - chr13:32338301 9.9 3570 358.8
22:54:12.488 INFO ProgressMeter - chr13:48307278 10.1 3630 358.6
22:54:22.951 INFO ProgressMeter - chr13:102295837 10.3 3720 361.3
22:54:33.433 INFO ProgressMeter - chr13:113310707 10.5 3800 362.9
22:54:44.421 INFO ProgressMeter - chr14:37588451 10.7 3870 363.2
22:54:55.302 INFO ProgressMeter - chr14:68497445 10.8 3950 364.6
22:55:06.432 INFO ProgressMeter - chr14:102084679 11.0 4020 364.8
22:55:18.425 INFO ProgressMeter - chr15:34347603 11.2 4090 364.5
22:55:28.714 INFO ProgressMeter - chr15:41710689 11.4 4140 363.4
22:55:39.540 INFO ProgressMeter - chr15:49434066 11.6 4200 362.9
22:55:51.706 INFO ProgressMeter - chr15:88032855 11.8 4290 364.3
22:56:03.087 INFO ProgressMeter - chr15:90760592 12.0 4380 366.1
22:56:13.425 INFO ProgressMeter - chr15:93002241 12.1 4450 366.6
22:56:23.887 INFO ProgressMeter - chr16:2071508 12.3 4520 367.1
22:56:35.090 INFO ProgressMeter - chr16:3592786 12.5 4620 369.6
22:56:45.743 INFO ProgressMeter - chr16:3810601 12.7 4680 369.2
22:56:56.221 INFO ProgressMeter - chr16:23624007 12.9 4750 369.6
22:57:06.301 INFO ProgressMeter - chr16:56836599 13.0 4820 370.2
22:57:18.466 INFO ProgressMeter - chr16:72793316 13.2 4880 369.1
22:57:29.209 INFO ProgressMeter - chr16:72959364 13.4 4920 367.2
22:57:41.126 INFO ProgressMeter - chr16:89282758 13.6 5000 367.7
22:57:51.367 INFO ProgressMeter - chr16:89799603 13.8 5070 368.2
22:58:02.256 INFO ProgressMeter - chr17:7675482 14.0 5130 367.7
22:58:13.096 INFO ProgressMeter - chr17:16057512 14.1 5210 368.7
22:58:23.940 INFO ProgressMeter - chr17:31169889 14.3 5290 369.6
22:58:35.500 INFO ProgressMeter - chr17:35118499 14.5 5380 370.9
22:58:45.792 INFO ProgressMeter - chr17:39711993 14.7 5440 370.7
22:58:56.796 INFO ProgressMeter - chr17:40389963 14.9 5510 370.8
22:59:07.699 INFO ProgressMeter - chr17:42338729 15.0 5610 373.0
22:59:18.114 INFO ProgressMeter - chr17:43094813 15.2 5670 372.6
22:59:28.344 INFO ProgressMeter - chr17:43534630 15.4 5720 371.8
22:59:39.012 INFO ProgressMeter - chr17:43542630 15.6 5770 370.7
22:59:49.159 INFO ProgressMeter - chr17:45273501 15.7 5800 368.7
22:59:59.443 INFO ProgressMeter - chr17:59896825 15.9 5870 369.1
23:00:10.007 INFO ProgressMeter - chr17:61776399 16.1 5940 369.4
23:00:20.374 INFO ProgressMeter - chr17:72126258 16.3 6010 369.8
23:00:30.816 INFO ProgressMeter - chr18:42004486 16.4 6110 371.9
23:00:41.945 INFO ProgressMeter - chr18:51067017 16.6 6180 372.0
23:00:52.409 INFO ProgressMeter - chr19:2216383 16.8 6280 374.1
23:01:02.924 INFO ProgressMeter - chr19:5240197 17.0 6380 376.1
23:01:12.970 INFO ProgressMeter - chr19:10156439 17.1 6450 376.5
23:01:24.057 INFO ProgressMeter - chr19:12943711 17.3 6540 377.7
23:01:34.784 INFO ProgressMeter - chr19:15238741 17.5 6610 377.9
23:01:45.259 INFO ProgressMeter - chr19:19146740 17.7 6690 378.7
23:01:56.519 INFO ProgressMeter - chr19:35723729 17.9 6770 379.2
23:02:07.049 INFO ProgressMeter - chr19:40282168 18.0 6850 379.9
23:02:18.085 INFO ProgressMeter - chr19:42291556 18.2 6910 379.4
23:02:28.948 INFO ProgressMeter - chr19:45411357 18.4 7000 380.5
23:02:38.972 INFO ProgressMeter - chr19:52222097 18.6 7080 381.4
23:02:49.745 INFO ProgressMeter - chr2:17768736 18.7 7130 380.4
23:03:00.698 INFO ProgressMeter - chr2:25878164 18.9 7200 380.4
23:03:12.055 INFO ProgressMeter - chr2:29226180 19.1 7250 379.3
23:03:23.155 INFO ProgressMeter - chr2:29911842 19.3 7300 378.2
23:03:34.379 INFO ProgressMeter - chr2:47408399 19.5 7360 377.7
23:03:44.797 INFO ProgressMeter - chr2:47806777 19.7 7400 376.4
23:03:56.345 INFO ProgressMeter - chr2:96253997 19.9 7460 375.8
23:04:06.901 INFO ProgressMeter - chr2:108773045 20.0 7540 376.5
23:04:19.227 INFO ProgressMeter - chr2:111128793 20.2 7570 374.1
23:04:32.195 INFO ProgressMeter - chr2:113227347 20.5 7620 372.6
23:04:43.376 INFO ProgressMeter - chr2:113233287 20.6 7650 370.7
23:04:53.960 INFO ProgressMeter - chr2:140233184 20.8 7710 370.4
23:05:04.239 INFO ProgressMeter - chr2:140868097 21.0 7790 371.2
23:05:14.957 INFO ProgressMeter - chr2:177234003 21.2 7860 371.4
23:05:26.102 INFO ProgressMeter - chr2:201285277 21.3 7950 372.4
23:05:37.244 INFO ProgressMeter - chr2:222199885 21.5 8030 372.9
23:05:49.040 INFO ProgressMeter - chr2:222206432 21.7 8070 371.4
23:06:00.953 INFO ProgressMeter - chr2:222215546 21.9 8120 370.3
23:06:12.108 INFO ProgressMeter - chr2:222298829 22.1 8160 369.0
23:06:23.182 INFO ProgressMeter - chr20:15144220 22.3 8230 369.1
23:06:34.050 INFO ProgressMeter - chr20:37386115 22.5 8300 369.2
23:06:45.753 INFO ProgressMeter - chr20:47647071 22.7 8390 370.0
23:06:56.355 INFO ProgressMeter - chr20:58903670 22.9 8450 369.8
23:07:06.618 INFO ProgressMeter - chr21:38423408 23.0 8520 370.1
23:07:17.390 INFO ProgressMeter - chr21:41489990 23.2 8570 369.3
23:07:28.064 INFO ProgressMeter - chr21:41493083 23.4 8590 367.4
23:07:40.367 INFO ProgressMeter - chr21:41503877 23.6 8630 365.9
23:07:51.596 INFO ProgressMeter - chr22:20982500 23.8 8690 365.5
23:08:04.856 INFO ProgressMeter - chr22:23291795 24.0 8760 365.1
23:08:16.229 INFO ProgressMeter - chr22:29282727 24.2 8850 365.9
23:08:26.704 INFO ProgressMeter - chr22:29299597 24.4 8890 365.0
23:08:37.060 INFO ProgressMeter - chr22:41168447 24.5 8960 365.2
23:08:48.175 INFO ProgressMeter - chr3:10141846 24.7 9030 365.3
23:08:58.497 INFO ProgressMeter - chr3:12357327 24.9 9070 364.4
23:09:09.225 INFO ProgressMeter - chr3:12364330 25.1 9110 363.4
23:09:20.171 INFO ProgressMeter - chr3:12373559 25.2 9160 362.8
23:09:31.773 INFO ProgressMeter - chr3:12585679 25.4 9210 362.0
23:09:42.733 INFO ProgressMeter - chr3:37048902 25.6 9290 362.5
23:09:52.839 INFO ProgressMeter - chr3:47086193 25.8 9350 362.5
23:10:02.891 INFO ProgressMeter - chr3:49687147 26.0 9410 362.5
23:10:13.920 INFO ProgressMeter - chr3:52579052 26.1 9480 362.6
23:10:23.986 INFO ProgressMeter - chr3:72446494 26.3 9550 362.9
23:10:35.072 INFO ProgressMeter - chr3:135201472 26.5 9630 363.4
23:10:45.098 INFO ProgressMeter - chr3:138704441 26.7 9700 363.8
23:10:55.163 INFO ProgressMeter - chr3:142555875 26.8 9780 364.5
23:11:06.111 INFO ProgressMeter - chr3:179220984 27.0 9860 365.0
23:11:16.868 INFO ProgressMeter - chr3:185473699 27.2 9930 365.1
23:11:27.191 INFO ProgressMeter - chr3:187731707 27.4 9990 365.0
23:11:37.971 INFO ProgressMeter - chr4:1799745 27.5 10080 365.9
23:11:48.320 INFO ProgressMeter - chr4:20617437 27.7 10160 366.5
23:12:00.502 INFO ProgressMeter - chr4:54277386 27.9 10230 366.4
23:12:10.701 INFO ProgressMeter - chr4:54714776 28.1 10290 366.3
23:12:21.531 INFO ProgressMeter - chr4:54738512 28.3 10320 365.0
23:12:32.429 INFO ProgressMeter - chr4:80274907 28.5 10400 365.5
23:12:43.864 INFO ProgressMeter - chr4:105238704 28.6 10470 365.5
23:12:54.235 INFO ProgressMeter - chr4:122867753 28.8 10530 365.4
23:13:05.766 INFO ProgressMeter - chr4:186597138 29.0 10610 365.7
23:13:16.899 INFO ProgressMeter - chr4:186707582 29.2 10660 365.1
23:13:27.301 INFO ProgressMeter - chr5:38957650 29.4 10730 365.4
23:13:37.795 INFO ProgressMeter - chr5:56881081 29.5 10820 366.2
23:13:49.093 INFO ProgressMeter - chr5:80864811 29.7 10900 366.6
23:13:59.584 INFO ProgressMeter - chr5:112838451 29.9 10970 366.8
23:14:11.121 INFO ProgressMeter - chr5:122463489 30.1 11020 366.1
23:14:21.956 INFO ProgressMeter - chr5:142656309 30.3 11100 366.6
23:14:33.358 INFO ProgressMeter - chr5:150114836 30.5 11160 366.3
23:14:43.888 INFO ProgressMeter - chr5:156235227 30.6 11230 366.5
23:14:55.511 INFO ProgressMeter - chr5:177093652 30.8 11290 366.1
23:15:07.435 INFO ProgressMeter - chr5:177235819 31.0 11330 365.0
23:15:17.802 INFO ProgressMeter - chr5:180620607 31.2 11400 365.3
23:15:28.813 INFO ProgressMeter - chr6:20485051 31.4 11490 366.0
23:15:40.605 INFO ProgressMeter - chr6:29942755 31.6 11550 365.6
23:15:52.144 INFO ProgressMeter - chr6:30712772 31.8 11590 364.7
23:16:02.739 INFO ProgressMeter - chr6:32223854 32.0 11650 364.5
23:16:13.022 INFO ProgressMeter - chr6:41957153 32.1 11720 364.8
23:16:23.589 INFO ProgressMeter - chr6:106105235 32.3 11810 365.6
23:16:34.769 INFO ProgressMeter - chr6:117321729 32.5 11870 365.3
23:16:44.895 INFO ProgressMeter - chr6:117330597 32.7 11910 364.6
23:16:56.785 INFO ProgressMeter - chr6:117353074 32.9 11970 364.3
23:17:07.968 INFO ProgressMeter - chr6:135195746 33.0 12040 364.3
23:17:21.648 INFO ProgressMeter - chr6:135208602 33.3 12090 363.3
23:17:34.200 INFO ProgressMeter - chr6:135213648 33.5 12120 362.0
23:17:45.788 INFO ProgressMeter - chr6:137878594 33.7 12170 361.4
23:17:57.315 INFO ProgressMeter - chr6:151989140 33.9 12230 361.1
23:18:08.741 INFO ProgressMeter - chr6:157207104 34.1 12290 360.8
23:18:19.148 INFO ProgressMeter - chr7:2913285 34.2 12370 361.4
23:18:29.583 INFO ProgressMeter - chr7:13895026 34.4 12440 361.6
23:18:40.399 INFO ProgressMeter - chr7:13933920 34.6 12480 360.8
23:18:51.387 INFO ProgressMeter - chr7:13943133 34.8 12540 360.7
23:19:06.720 INFO ProgressMeter - chr7:13950980 35.0 12580 359.2
23:19:17.176 INFO ProgressMeter - chr7:13958322 35.2 12620 358.5
23:19:28.917 INFO ProgressMeter - chr7:13965796 35.4 12660 357.7
23:19:42.435 INFO ProgressMeter - chr7:13976046 35.6 12720 357.1
23:19:54.167 INFO ProgressMeter - chr7:13983762 35.8 12770 356.5
23:20:05.328 INFO ProgressMeter - chr7:41689948 36.0 12810 355.8
23:20:16.950 INFO ProgressMeter - chr7:55161762 36.2 12870 355.6
23:20:27.988 INFO ProgressMeter - chr7:55173975 36.4 12910 354.9
23:20:39.720 INFO ProgressMeter - chr7:55198715 36.6 12960 354.3
23:20:50.341 INFO ProgressMeter - chr7:81762705 36.8 13030 354.5
23:21:00.408 INFO ProgressMeter - chr7:102197213 36.9 13100 354.8
23:21:12.246 INFO ProgressMeter - chr7:116740004 37.1 13170 354.8
23:21:24.227 INFO ProgressMeter - chr7:129208757 37.3 13230 354.5
23:21:35.237 INFO ProgressMeter - chr7:140794077 37.5 13300 354.7
23:21:45.733 INFO ProgressMeter - chr7:151467117 37.7 13390 355.4
23:21:57.535 INFO ProgressMeter - chr7:152181909 37.9 13450 355.1
23:22:07.891 INFO ProgressMeter - chr8:26354466 38.0 13540 355.9
23:22:19.172 INFO ProgressMeter - chr8:32760198 38.2 13610 356.0
23:22:29.174 INFO ProgressMeter - chr8:38428350 38.4 13680 356.3
23:22:40.843 INFO ProgressMeter - chr8:47778726 38.6 13740 356.0
23:22:51.093 INFO ProgressMeter - chr8:47930670 38.8 13810 356.2
23:23:01.506 INFO ProgressMeter - chr8:73955909 38.9 13900 357.0
23:23:13.519 INFO ProgressMeter - chr8:127735568 39.1 13970 356.9
23:23:24.910 INFO ProgressMeter - chr9:5054861 39.3 14060 357.5
23:23:35.327 INFO ProgressMeter - chr9:8504357 39.5 14140 358.0
23:23:46.164 INFO ProgressMeter - chr9:36930886 39.7 14210 358.1
23:23:59.269 INFO ProgressMeter - chr9:84743137 39.9 14290 358.1
23:24:13.071 INFO ProgressMeter - chr9:84861338 40.1 14330 357.1
23:24:23.805 INFO ProgressMeter - chr9:84866093 40.3 14360 356.2
23:24:35.343 INFO ProgressMeter - chr9:85020272 40.5 14410 355.8
23:24:45.572 INFO ProgressMeter - chr9:85026970 40.7 14440 355.0
23:24:56.317 INFO ProgressMeter - chr9:99142534 40.9 14520 355.4
23:25:07.250 INFO ProgressMeter - chr9:130887504 41.0 14590 355.6
23:25:17.355 INFO ProgressMeter - chr9:136507351 41.2 14650 355.6
23:25:28.172 INFO ProgressMeter - chrX:40064509 41.4 14740 356.2
23:25:38.927 INFO ProgressMeter - chrX:47179878 41.6 14810 356.3
23:25:50.416 INFO ProgressMeter - chrX:49035511 41.8 14880 356.4
23:26:01.485 INFO ProgressMeter - chrX:53214687 41.9 14940 356.2
23:26:15.122 INFO ProgressMeter - chrX:67545450 42.2 15000 355.7
23:26:25.555 INFO ProgressMeter - chrX:71129769 42.3 15080 356.2
23:26:35.654 INFO ProgressMeter - chrX:71454739 42.5 15140 356.2
23:26:45.661 INFO ProgressMeter - chrX:101358615 42.7 15210 356.4
23:26:56.211 INFO ProgressMeter - chrX:130013588 42.9 15300 357.1
23:27:02.720 INFO Mutect2 - 761122 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
109 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
761231 total reads filtered out of 105880193 reads processed
23:27:02.721 INFO ProgressMeter - chrY:19567332 43.0 15378 358.0
23:27:02.721 INFO ProgressMeter - Traversal complete. Processed 15378 total regions in 43.0 minutes.
23:27:02.738 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 6.772067755
23:27:02.738 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 261.831531741
23:27:02.738 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 9.86 sec
23:27:02.739 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:27:02 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 42.97 minutes.
Runtime.totalMemory()=6509559808
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 LS0923_tumor.bam --tumor-sample LS0923 -L TST500C_manifest.bed -O LS0923.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:27:04.451 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
23:27:04.579 INFO FilterMutectCalls - ------------------------------------------------------------
23:27:04.582 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:27:04.582 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:27:04.582 INFO FilterMutectCalls - Executing as ?@nf-c232a592e17e15d2e40c57697f4e52d7-81a8e-wz48l on Linux v6.12.88 amd64
23:27:04.582 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:27:04.582 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:27:04 PM GMT
23:27:04.582 INFO FilterMutectCalls - ------------------------------------------------------------
23:27:04.582 INFO FilterMutectCalls - ------------------------------------------------------------
23:27:04.583 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:27:04.583 INFO FilterMutectCalls - Picard Version: 3.1.1
23:27:04.583 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:27:04.583 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:27:04.583 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:27:04.584 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:27:04.584 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:27:04.584 INFO FilterMutectCalls - Deflater: IntelDeflater
23:27:04.584 INFO FilterMutectCalls - Inflater: IntelInflater
23:27:04.584 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:27:04.584 INFO FilterMutectCalls - Requester pays: disabled
23:27:04.584 INFO FilterMutectCalls - Initializing engine
23:27:04.713 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.hCEJhDZ57F/LS0923.mutect2.raw.vcf.gz
23:27:04.826 INFO FilterMutectCalls - Done initializing engine
23:27:04.890 INFO ProgressMeter - Starting traversal
23:27:04.891 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:27:04.892 INFO FilterMutectCalls - Starting pass 0 through the variants
23:27:06.257 INFO FilterMutectCalls - Finished pass 0 through the variants
23:27:08.463 INFO FilterMutectCalls - Starting pass 1 through the variants
23:27:09.941 INFO FilterMutectCalls - Finished pass 1 through the variants
23:27:10.353 INFO FilterMutectCalls - Starting pass 2 through the variants
23:27:11.791 INFO FilterMutectCalls - Finished pass 2 through the variants
23:27:11.793 INFO FilterMutectCalls - Starting pass 3 through the variants
23:27:13.040 INFO FilterMutectCalls - Finished pass 3 through the variants
23:27:13.048 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:27:13.049 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:27:13.049 INFO ProgressMeter - chr7:13952835 0.1 11544 84903.2
23:27:13.049 INFO ProgressMeter - Traversal complete. Processed 11544 total variants in 0.1 minutes.
23:27:13.060 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:27:13 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=318767104
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 LS0923.mutect2.raw.vcf.gz --stats LS0923.mutect2.raw.vcf.gz.stats -O LS0923.mutect2.filtered.vcf.gz
23:27:14.427 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
23:27:14.546 INFO SelectVariants - ------------------------------------------------------------
23:27:14.549 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:27:14.549 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:27:14.549 INFO SelectVariants - Executing as ?@nf-c232a592e17e15d2e40c57697f4e52d7-81a8e-wz48l on Linux v6.12.88 amd64
23:27:14.549 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:27:14.550 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:27:14 PM GMT
23:27:14.550 INFO SelectVariants - ------------------------------------------------------------
23:27:14.550 INFO SelectVariants - ------------------------------------------------------------
23:27:14.550 INFO SelectVariants - HTSJDK Version: 4.1.0
23:27:14.550 INFO SelectVariants - Picard Version: 3.1.1
23:27:14.551 INFO SelectVariants - Built for Spark Version: 3.5.0
23:27:14.551 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:27:14.551 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:27:14.551 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:27:14.551 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:27:14.551 INFO SelectVariants - Deflater: IntelDeflater
23:27:14.551 INFO SelectVariants - Inflater: IntelInflater
23:27:14.551 INFO SelectVariants - GCS max retries/reopens: 20
23:27:14.551 INFO SelectVariants - Requester pays: disabled
23:27:14.552 INFO SelectVariants - Initializing engine
23:27:14.719 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.hCEJhDZ57F/LS0923.mutect2.filtered.vcf.gz
23:27:14.828 INFO SelectVariants - Done initializing engine
23:27:14.867 INFO ProgressMeter - Starting traversal
23:27:14.867 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:27:14.956 INFO ProgressMeter - chr6:29942825 0.0 2886 1990344.8
23:27:14.956 INFO ProgressMeter - Traversal complete. Processed 2886 total variants in 0.0 minutes.
23:27:14.969 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:27:14 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 LS0923.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0923.mutect2.pass.vcf.gz