Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0898/LS0898_tumor.bam.bai
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/30/e9aafcd75ca1aac2cc5f53546a3786/.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/30/e9aafcd75ca1aac2cc5f53546a3786/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0898/LS0898_tumor.bam
==> STAGING COMPLETE (10 inputs)
22:44:11.947 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
22:44:12.048 INFO Mutect2 - ------------------------------------------------------------
22:44:12.050 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:12.050 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:12.050 INFO Mutect2 - Executing as ?@nf-30e9aafcd75ca1aac2cc5f53546a3786-af43f-dqxhj on Linux v6.12.88 amd64
22:44:12.050 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:12.050 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:11 PM GMT
22:44:12.050 INFO Mutect2 - ------------------------------------------------------------
22:44:12.050 INFO Mutect2 - ------------------------------------------------------------
22:44:12.051 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:12.051 INFO Mutect2 - Picard Version: 3.1.1
22:44:12.051 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:12.051 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:12.051 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:12.052 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:12.052 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:12.052 INFO Mutect2 - Deflater: IntelDeflater
22:44:12.052 INFO Mutect2 - Inflater: IntelInflater
22:44:12.052 INFO Mutect2 - GCS max retries/reopens: 20
22:44:12.052 INFO Mutect2 - Requester pays: disabled
22:44:12.052 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.7uY8br2qWj/LS0898_tumor.bam.bai is older than BAM /tmp/nxf.7uY8br2qWj/LS0898_tumor.bam
22:44:12.206 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.7uY8br2qWj/af-only-gnomad.hg38.vcf.gz
22:44:12.369 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.7uY8br2qWj/TST500C_manifest.bed
22:44:12.418 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:12.447 INFO Mutect2 - Done initializing engine
22:44:12.459 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
22:44:12.461 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
22:44:12.461 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:12.461 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:12.472 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
22:44:12.480 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:12.481 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:12.481 INFO IntelPairHmm - Available threads: 384
22:44:12.481 INFO IntelPairHmm - Requested threads: 4
22:44:12.481 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:12.513 INFO ProgressMeter - Starting traversal
22:44:12.513 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:23.607 INFO ProgressMeter - chr1:9723967 0.2 60 324.6
22:44:34.603 INFO ProgressMeter - chr1:11231298 0.4 120 325.9
22:44:46.271 INFO ProgressMeter - chr1:15930305 0.6 180 319.9
22:44:56.691 INFO ProgressMeter - chr1:15937385 0.7 220 298.8
22:45:07.583 INFO ProgressMeter - chr1:18746722 0.9 270 294.2
22:45:18.573 INFO ProgressMeter - chr1:26773578 1.1 330 299.7
22:45:29.141 INFO ProgressMeter - chr1:36472313 1.3 380 297.5
22:45:39.939 INFO ProgressMeter - chr1:39902153 1.5 440 302.0
22:45:50.352 INFO ProgressMeter - chr1:46248510 1.6 510 312.8
22:46:01.794 INFO ProgressMeter - chr1:64886257 1.8 580 318.4
22:46:12.128 INFO ProgressMeter - chr1:117153089 2.0 660 331.1
22:46:23.002 INFO ProgressMeter - chr1:119922634 2.2 710 326.5
22:46:34.416 INFO ProgressMeter - chr1:156868102 2.4 780 329.8
22:46:45.419 INFO ProgressMeter - chr1:156873723 2.5 800 313.9
22:46:55.492 INFO ProgressMeter - chr1:158612815 2.7 830 305.6
22:47:07.233 INFO ProgressMeter - chr1:158667897 2.9 890 305.6
22:47:17.336 INFO ProgressMeter - chr1:175988286 3.1 950 308.4
22:47:28.152 INFO ProgressMeter - chr1:193212063 3.3 1020 312.8
22:47:38.939 INFO ProgressMeter - chr1:204469727 3.4 1080 313.9
22:47:49.847 INFO ProgressMeter - chr1:206474329 3.6 1140 314.7
22:48:00.709 INFO ProgressMeter - chr1:226390456 3.8 1210 318.1
22:48:12.298 INFO ProgressMeter - chr1:243502699 4.0 1260 315.3
22:48:23.093 INFO ProgressMeter - chr10:8073824 4.2 1310 313.7
22:48:33.504 INFO ProgressMeter - chr10:27061123 4.3 1360 312.7
22:48:43.953 INFO ProgressMeter - chr10:32028426 4.5 1410 311.7
22:48:55.013 INFO ProgressMeter - chr10:43113009 4.7 1470 312.2
22:49:06.010 INFO ProgressMeter - chr10:43117481 4.9 1510 308.7
22:49:16.056 INFO ProgressMeter - chr10:62092453 5.1 1560 308.4
22:49:27.387 INFO ProgressMeter - chr10:68691171 5.2 1610 306.8
22:49:40.907 INFO ProgressMeter - chr10:101772101 5.5 1700 310.6
22:49:51.053 INFO ProgressMeter - chr10:110590970 5.6 1780 315.5
22:50:03.265 INFO ProgressMeter - chr10:121480873 5.8 1840 314.8
22:50:14.434 INFO ProgressMeter - chr10:121521300 6.0 1890 313.3
22:50:26.030 INFO ProgressMeter - chr11:22625162 6.2 1960 314.8
22:50:36.044 INFO ProgressMeter - chr11:67429118 6.4 2040 319.1
22:50:48.137 INFO ProgressMeter - chr11:69701108 6.6 2120 321.5
22:50:58.595 INFO ProgressMeter - chr11:69775515 6.8 2180 322.1
22:51:11.004 INFO ProgressMeter - chr11:69813032 7.0 2210 316.9
22:51:22.017 INFO ProgressMeter - chr11:76546209 7.2 2270 317.1
22:51:34.051 INFO ProgressMeter - chr11:77429651 7.4 2330 316.6
22:51:44.790 INFO ProgressMeter - chr11:102209515 7.5 2410 319.7
22:51:55.735 INFO ProgressMeter - chr11:108250768 7.7 2440 316.0
22:52:06.838 INFO ProgressMeter - chr11:118471782 7.9 2530 320.0
22:52:19.753 INFO ProgressMeter - chr11:118503436 8.1 2590 318.9
22:52:31.636 INFO ProgressMeter - chr11:119285187 8.3 2640 317.4
22:52:42.019 INFO ProgressMeter - chr11:125644774 8.5 2680 315.6
22:53:00.323 INFO ProgressMeter - chr11:128460025 8.8 2720 309.2
22:53:11.940 INFO ProgressMeter - chr11:128781956 9.0 2760 307.0
22:53:22.761 INFO ProgressMeter - chr12:307767 9.2 2800 305.3
22:53:33.747 INFO ProgressMeter - chr12:4369025 9.4 2870 306.8
22:53:44.965 INFO ProgressMeter - chr12:4432441 9.5 2920 306.1
22:53:55.763 INFO ProgressMeter - chr12:6570674 9.7 2960 304.5
22:54:06.018 INFO ProgressMeter - chr12:6601646 9.9 3010 304.3
22:54:19.418 INFO ProgressMeter - chr12:11857029 10.1 3050 301.5
22:54:34.081 INFO ProgressMeter - chr12:11861886 10.4 3090 298.3
22:54:45.088 INFO ProgressMeter - chr12:11866156 10.5 3120 295.9
22:54:55.992 INFO ProgressMeter - chr12:11890920 10.7 3150 293.7
22:55:07.650 INFO ProgressMeter - chr12:25227544 10.9 3230 295.8
22:55:18.860 INFO ProgressMeter - chr12:45850483 11.1 3280 295.3
22:55:30.552 INFO ProgressMeter - chr12:49031609 11.3 3340 295.6
22:55:41.961 INFO ProgressMeter - chr12:49037658 11.5 3370 293.3
22:55:54.013 INFO ProgressMeter - chr12:49049680 11.7 3420 292.5
22:56:04.387 INFO ProgressMeter - chr12:50090239 11.9 3470 292.5
22:56:15.180 INFO ProgressMeter - chr12:56094097 12.0 3530 293.1
22:56:27.322 INFO ProgressMeter - chr12:57094618 12.2 3580 292.3
22:56:37.351 INFO ProgressMeter - chr12:57748124 12.4 3630 292.4
22:56:47.591 INFO ProgressMeter - chr12:68830063 12.6 3700 294.0
22:56:57.658 INFO ProgressMeter - chr12:105934409 12.8 3750 294.1
22:57:08.113 INFO ProgressMeter - chr12:120099028 12.9 3810 294.7
22:57:19.162 INFO ProgressMeter - chr12:132642504 13.1 3860 294.4
22:57:30.843 INFO ProgressMeter - chr13:20979689 13.3 3920 294.6
22:57:41.260 INFO ProgressMeter - chr13:21688777 13.5 3960 293.8
22:57:52.610 INFO ProgressMeter - chr13:28100466 13.7 4030 294.8
22:58:09.785 INFO ProgressMeter - chr13:28388492 14.0 4080 292.4
22:58:21.840 INFO ProgressMeter - chr13:32332812 14.2 4130 291.8
22:58:33.231 INFO ProgressMeter - chr13:32356489 14.3 4170 290.7
22:58:43.358 INFO ProgressMeter - chr13:48347823 14.5 4230 291.4
22:58:54.836 INFO ProgressMeter - chr13:101937546 14.7 4310 293.1
22:59:06.963 INFO ProgressMeter - chr13:102873257 14.9 4370 293.1
22:59:17.816 INFO ProgressMeter - chr13:113308537 15.1 4430 293.6
22:59:28.068 INFO ProgressMeter - chr14:23308028 15.3 4470 292.9
22:59:38.768 INFO ProgressMeter - chr14:37590392 15.4 4530 293.4
22:59:48.793 INFO ProgressMeter - chr14:37599003 15.6 4580 293.5
23:00:00.141 INFO ProgressMeter - chr14:81143621 15.8 4640 293.8
23:00:11.452 INFO ProgressMeter - chr14:98379232 16.0 4690 293.4
23:00:23.873 INFO ProgressMeter - chr15:32740944 16.2 4750 293.4
23:00:36.467 INFO ProgressMeter - chr15:34356421 16.4 4790 292.1
23:00:46.721 INFO ProgressMeter - chr15:41669793 16.6 4820 290.9
23:00:57.267 INFO ProgressMeter - chr15:41743085 16.7 4860 290.2
23:01:09.077 INFO ProgressMeter - chr15:49427560 16.9 4900 289.2
23:01:19.411 INFO ProgressMeter - chr15:67166777 17.1 4970 290.4
23:01:31.257 INFO ProgressMeter - chr15:88032855 17.3 5020 290.0
23:01:41.425 INFO ProgressMeter - chr15:89303862 17.5 5080 290.6
23:01:51.703 INFO ProgressMeter - chr15:90769436 17.7 5130 290.6
23:02:02.723 INFO ProgressMeter - chr15:92985561 17.8 5190 291.0
23:02:13.022 INFO ProgressMeter - chr15:98922367 18.0 5240 291.0
23:02:23.790 INFO ProgressMeter - chr16:2062562 18.2 5300 291.4
23:02:34.413 INFO ProgressMeter - chr16:2175299 18.4 5360 291.9
23:02:44.985 INFO ProgressMeter - chr16:3596263 18.5 5420 292.3
23:02:55.009 INFO ProgressMeter - chr16:3729298 18.7 5450 291.3
23:03:05.815 INFO ProgressMeter - chr16:5818645 18.9 5510 291.7
23:03:16.324 INFO ProgressMeter - chr16:11255310 19.1 5550 291.1
23:03:27.846 INFO ProgressMeter - chr16:23635837 19.3 5600 290.8
23:03:39.043 INFO ProgressMeter - chr16:56831907 19.4 5670 291.6
23:03:49.368 INFO ProgressMeter - chr16:68823397 19.6 5730 292.1
23:03:59.861 INFO ProgressMeter - chr16:72794511 19.8 5760 291.1
23:04:11.800 INFO ProgressMeter - chr16:72811903 20.0 5790 289.7
23:04:21.895 INFO ProgressMeter - chr16:77983098 20.2 5820 288.7
23:04:34.684 INFO ProgressMeter - chr16:89281427 20.4 5890 289.2
23:04:45.211 INFO ProgressMeter - chr16:89288526 20.5 5920 288.1
23:04:55.833 INFO ProgressMeter - chr17:7314289 20.7 6000 289.5
23:05:09.248 INFO ProgressMeter - chr17:7676526 20.9 6040 288.4
23:05:19.800 INFO ProgressMeter - chr17:16064868 21.1 6120 289.8
23:05:30.304 INFO ProgressMeter - chr17:18045145 21.3 6190 290.7
23:05:40.318 INFO ProgressMeter - chr17:31349118 21.5 6260 291.7
23:05:50.887 INFO ProgressMeter - chr17:39519954 21.6 6330 292.5
23:06:02.167 INFO ProgressMeter - chr17:39723317 21.8 6390 292.7
23:06:12.869 INFO ProgressMeter - chr17:40416420 22.0 6460 293.6
23:06:23.685 INFO ProgressMeter - chr17:43045746 22.2 6550 295.2
23:06:35.472 INFO ProgressMeter - chr17:43094246 22.4 6610 295.3
23:06:47.137 INFO ProgressMeter - chr17:43532346 22.6 6660 295.0
23:06:59.991 INFO ProgressMeter - chr17:43539570 22.8 6710 294.4
23:07:14.433 INFO ProgressMeter - chr17:43543970 23.0 6740 292.6
23:07:25.140 INFO ProgressMeter - chr17:48734639 23.2 6790 292.5
23:07:35.673 INFO ProgressMeter - chr17:59896055 23.4 6850 292.9
23:07:46.663 INFO ProgressMeter - chr17:60663499 23.6 6920 293.6
23:07:56.730 INFO ProgressMeter - chr17:65537569 23.7 6980 294.1
23:08:07.710 INFO ProgressMeter - chr17:80880413 23.9 7050 294.7
23:08:18.403 INFO ProgressMeter - chr18:42027441 24.1 7130 295.9
23:08:30.862 INFO ProgressMeter - chr18:45063574 24.3 7180 295.4
23:08:41.820 INFO ProgressMeter - chr18:63318609 24.5 7250 296.1
23:08:52.871 INFO ProgressMeter - chr19:2226181 24.7 7330 297.1
23:09:03.677 INFO ProgressMeter - chr19:5211588 24.9 7400 297.8
23:09:15.186 INFO ProgressMeter - chr19:7150495 25.0 7470 298.3
23:09:25.796 INFO ProgressMeter - chr19:10159840 25.2 7530 298.6
23:09:35.851 INFO ProgressMeter - chr19:10989315 25.4 7580 298.6
23:09:47.981 INFO ProgressMeter - chr19:14516199 25.6 7650 298.9
23:09:58.429 INFO ProgressMeter - chr19:15180142 25.8 7700 298.9
23:10:10.798 INFO ProgressMeter - chr19:15243240 26.0 7750 298.4
23:10:23.329 INFO ProgressMeter - chr19:18160469 26.2 7810 298.3
23:10:34.700 INFO ProgressMeter - chr19:29819287 26.4 7880 298.8
23:10:45.285 INFO ProgressMeter - chr19:35722689 26.5 7940 299.1
23:10:56.006 INFO ProgressMeter - chr19:40230314 26.7 8000 299.3
23:11:07.013 INFO ProgressMeter - chr19:41248512 26.9 8070 299.9
23:11:19.440 INFO ProgressMeter - chr19:41877303 27.1 8100 298.7
23:11:30.769 INFO ProgressMeter - chr19:42294984 27.3 8160 298.9
23:11:40.787 INFO ProgressMeter - chr19:45370414 27.5 8220 299.2
23:11:51.139 INFO ProgressMeter - chr19:47223744 27.6 8280 299.5
23:12:05.516 INFO ProgressMeter - chr2:15940559 27.9 8350 299.5
23:12:15.626 INFO ProgressMeter - chr2:15949795 28.1 8400 299.4
23:12:26.375 INFO ProgressMeter - chr2:25248035 28.2 8450 299.3
23:12:37.499 INFO ProgressMeter - chr2:25756016 28.4 8490 298.8
23:12:50.700 INFO ProgressMeter - chr2:29223893 28.6 8540 298.2
23:13:03.048 INFO ProgressMeter - chr2:29227572 28.8 8570 297.1
23:13:15.750 INFO ProgressMeter - chr2:42245503 29.1 8620 296.7
23:13:26.315 INFO ProgressMeter - chr2:47385164 29.2 8670 296.6
23:13:37.746 INFO ProgressMeter - chr2:47783457 29.4 8700 295.7
23:13:48.226 INFO ProgressMeter - chr2:60891681 29.6 8750 295.7
23:14:03.633 INFO ProgressMeter - chr2:96265136 29.9 8810 295.1
23:14:14.692 INFO ProgressMeter - chr2:108763835 30.0 8880 295.6
23:14:26.920 INFO ProgressMeter - chr2:111125787 30.2 8930 295.3
23:14:41.372 INFO ProgressMeter - chr2:111128819 30.5 8950 293.6
23:14:54.046 INFO ProgressMeter - chr2:113223769 30.7 8990 292.9
23:15:08.408 INFO ProgressMeter - chr2:113226980 30.9 9010 291.3
23:15:18.904 INFO ProgressMeter - chr2:113230966 31.1 9040 290.6
23:15:32.093 INFO ProgressMeter - chr2:113233757 31.3 9060 289.2
23:15:44.354 INFO ProgressMeter - chr2:127289687 31.5 9110 288.9
23:15:55.677 INFO ProgressMeter - chr2:140503053 31.7 9180 289.4
23:16:05.922 INFO ProgressMeter - chr2:140883815 31.9 9230 289.4
23:16:16.469 INFO ProgressMeter - chr2:172556149 32.1 9290 289.7
23:16:27.403 INFO ProgressMeter - chr2:191034546 32.2 9350 289.9
23:16:38.791 INFO ProgressMeter - chr2:201266617 32.4 9420 290.4
23:16:49.064 INFO ProgressMeter - chr2:211623970 32.6 9480 290.7
23:17:00.012 INFO ProgressMeter - chr2:222199966 32.8 9540 290.9
23:17:13.199 INFO ProgressMeter - chr2:222203944 33.0 9570 289.9
23:17:26.823 INFO ProgressMeter - chr2:222209118 33.2 9610 289.1
23:17:39.226 INFO ProgressMeter - chr2:222213993 33.4 9650 288.5
23:17:52.624 INFO ProgressMeter - chr2:222219521 33.7 9680 287.5
23:18:05.213 INFO ProgressMeter - chr2:226795692 33.9 9740 287.5
23:18:15.334 INFO ProgressMeter - chr20:9539533 34.0 9780 287.2
23:18:27.557 INFO ProgressMeter - chr20:32436587 34.3 9840 287.3
23:18:38.233 INFO ProgressMeter - chr20:42102122 34.4 9920 288.1
23:18:50.738 INFO ProgressMeter - chr20:47652929 34.6 9990 288.4
23:19:01.257 INFO ProgressMeter - chr20:58891755 34.8 10050 288.7
23:19:14.565 INFO ProgressMeter - chr21:38381774 35.0 10120 288.9
23:19:25.813 INFO ProgressMeter - chr21:38471902 35.2 10160 288.5
23:19:39.383 INFO ProgressMeter - chr21:41489217 35.4 10200 287.7
23:19:56.772 INFO ProgressMeter - chr21:41491834 35.7 10220 286.0
23:20:10.349 INFO ProgressMeter - chr21:41499201 36.0 10250 285.0
23:20:22.853 INFO ProgressMeter - chr21:41503040 36.2 10280 284.2
23:20:35.293 INFO ProgressMeter - chr21:41507732 36.4 10320 283.7
23:20:46.335 INFO ProgressMeter - chr22:20995961 36.6 10380 283.9
23:21:02.356 INFO ProgressMeter - chr22:23291042 36.8 10440 283.5
23:21:12.709 INFO ProgressMeter - chr22:28706967 37.0 10490 283.5
23:21:24.108 INFO ProgressMeter - chr22:29283499 37.2 10550 283.7
23:21:36.539 INFO ProgressMeter - chr22:29287096 37.4 10580 282.9
23:21:48.352 INFO ProgressMeter - chr22:41117436 37.6 10640 283.0
23:22:01.151 INFO ProgressMeter - chr22:47966508 37.8 10700 283.0
23:22:12.893 INFO ProgressMeter - chr3:12287896 38.0 10760 283.1
23:22:39.996 INFO ProgressMeter - chr3:12356231 38.5 10790 280.6
23:22:57.468 INFO ProgressMeter - chr3:12361013 38.7 10820 279.2
23:23:10.936 INFO ProgressMeter - chr3:12366524 39.0 10860 278.6
23:23:22.522 INFO ProgressMeter - chr3:12370809 39.2 10890 278.0
23:23:36.544 INFO ProgressMeter - chr3:12375299 39.4 10920 277.2
23:23:48.519 INFO ProgressMeter - chr3:12584512 39.6 10960 276.8
23:23:59.300 INFO ProgressMeter - chr3:12649648 39.8 11000 276.5
23:24:09.696 INFO ProgressMeter - chr3:41094711 40.0 11060 276.8
23:24:21.275 INFO ProgressMeter - chr3:47120455 40.1 11110 276.7
23:24:32.173 INFO ProgressMeter - chr3:49684403 40.3 11150 276.5
23:24:44.759 INFO ProgressMeter - chr3:49902844 40.5 11210 276.5
23:24:55.602 INFO ProgressMeter - chr3:52615349 40.7 11270 276.8
23:25:07.793 INFO ProgressMeter - chr3:72379249 40.9 11340 277.1
23:25:18.781 INFO ProgressMeter - chr3:119876411 41.1 11400 277.3
23:25:29.225 INFO ProgressMeter - chr3:135249334 41.3 11450 277.4
23:25:39.278 INFO ProgressMeter - chr3:136630849 41.4 11500 277.5
23:25:50.535 INFO ProgressMeter - chr3:142461938 41.6 11570 277.9
23:26:02.469 INFO ProgressMeter - chr3:142562808 41.8 11630 278.0
23:26:13.342 INFO ProgressMeter - chr3:179224079 42.0 11700 278.5
23:26:24.463 INFO ProgressMeter - chr3:185463548 42.2 11760 278.7
23:26:35.509 INFO ProgressMeter - chr3:186064415 42.4 11800 278.4
23:26:46.075 INFO ProgressMeter - chr3:189872907 42.6 11860 278.7
23:26:56.425 INFO ProgressMeter - chr3:196076091 42.7 11920 278.9
23:27:06.628 INFO ProgressMeter - chr4:20519380 42.9 11990 279.5
23:27:17.842 INFO ProgressMeter - chr4:54257096 43.1 12060 279.9
23:27:28.731 INFO ProgressMeter - chr4:54698282 43.3 12120 280.1
23:27:40.564 INFO ProgressMeter - chr4:54732108 43.5 12150 279.5
23:27:51.766 INFO ProgressMeter - chr4:80265187 43.7 12220 279.9
23:28:03.457 INFO ProgressMeter - chr4:105235163 43.8 12290 280.3
23:28:14.443 INFO ProgressMeter - chr4:105241330 44.0 12330 280.0
23:28:24.930 INFO ProgressMeter - chr4:106968597 44.2 12360 279.6
23:28:35.000 INFO ProgressMeter - chr4:142237862 44.4 12430 280.1
23:28:46.442 INFO ProgressMeter - chr4:186595687 44.6 12490 280.3
23:28:57.162 INFO ProgressMeter - chr4:186618641 44.7 12540 280.3
23:29:08.386 INFO ProgressMeter - chr4:186707949 44.9 12580 280.0
23:29:19.012 INFO ProgressMeter - chr5:35871209 45.1 12630 280.0
23:29:30.124 INFO ProgressMeter - chr5:44314782 45.3 12710 280.6
23:29:41.216 INFO ProgressMeter - chr5:56881990 45.5 12770 280.8
23:29:52.522 INFO ProgressMeter - chr5:80654859 45.7 12840 281.2
23:30:03.070 INFO ProgressMeter - chr5:112775627 45.8 12920 281.8
23:30:14.072 INFO ProgressMeter - chr5:112841243 46.0 12960 281.6
23:30:24.923 INFO ProgressMeter - chr5:122449843 46.2 13000 281.3
23:30:36.003 INFO ProgressMeter - chr5:138930895 46.4 13070 281.7
23:30:47.103 INFO ProgressMeter - chr5:142672821 46.6 13110 281.5
23:30:58.318 INFO ProgressMeter - chr5:150069980 46.8 13160 281.4
23:31:09.912 INFO ProgressMeter - chr5:150137178 47.0 13220 281.5
23:31:20.136 INFO ProgressMeter - chr5:161691939 47.1 13270 281.6
23:31:34.115 INFO ProgressMeter - chr5:177091746 47.4 13320 281.2
23:31:46.339 INFO ProgressMeter - chr5:177099907 47.6 13350 280.7
23:31:56.737 INFO ProgressMeter - chr5:177269600 47.7 13390 280.5
23:32:07.256 INFO ProgressMeter - chr5:179263687 47.9 13440 280.5
23:32:17.708 INFO ProgressMeter - chr6:20415963 48.1 13510 281.0
23:32:28.550 INFO ProgressMeter - chr6:20487966 48.3 13570 281.1
23:32:45.761 INFO ProgressMeter - chr6:29945449 48.6 13640 280.9
23:32:56.454 INFO ProgressMeter - chr6:30708231 48.7 13680 280.7
23:33:07.808 INFO ProgressMeter - chr6:32219590 48.9 13740 280.9
23:33:18.078 INFO ProgressMeter - chr6:33322860 49.1 13780 280.7
23:33:28.346 INFO ProgressMeter - chr6:41975393 49.3 13850 281.1
23:33:38.901 INFO ProgressMeter - chr6:106095613 49.4 13930 281.8
23:33:50.424 INFO ProgressMeter - chr6:117318336 49.6 13990 281.9
23:34:01.972 INFO ProgressMeter - chr6:117323571 49.8 14020 281.4
23:34:12.357 INFO ProgressMeter - chr6:117330291 50.0 14060 281.2
23:34:24.272 INFO ProgressMeter - chr6:117340483 50.2 14120 281.3
23:34:34.839 INFO ProgressMeter - chr6:135200083 50.4 14180 281.5
23:34:45.216 INFO ProgressMeter - chr6:135206648 50.5 14210 281.1
23:35:05.098 INFO ProgressMeter - chr6:135212997 50.9 14250 280.1
23:35:17.037 INFO ProgressMeter - chr6:135217041 51.1 14280 279.6
23:35:27.271 INFO ProgressMeter - chr6:149679922 51.2 14330 279.6
23:35:41.499 INFO ProgressMeter - chr6:151908902 51.5 14380 279.3
23:35:52.343 INFO ProgressMeter - chr6:157148622 51.7 14430 279.3
23:36:03.263 INFO ProgressMeter - chr6:161084499 51.8 14480 279.3
23:36:13.797 INFO ProgressMeter - chr7:2919370 52.0 14550 279.7
23:36:25.335 INFO ProgressMeter - chr7:13891895 52.2 14610 279.8
23:36:35.373 INFO ProgressMeter - chr7:13907342 52.4 14640 279.5
23:36:50.139 INFO ProgressMeter - chr7:13932720 52.6 14670 278.8
23:37:01.809 INFO ProgressMeter - chr7:13938835 52.8 14710 278.5
23:37:12.870 INFO ProgressMeter - chr7:13943475 53.0 14750 278.3
23:37:26.725 INFO ProgressMeter - chr7:13947803 53.2 14780 277.6
23:37:36.937 INFO ProgressMeter - chr7:13950855 53.4 14800 277.1
23:37:52.326 INFO ProgressMeter - chr7:13955514 53.7 14830 276.4
23:38:04.747 INFO ProgressMeter - chr7:13961048 53.9 14860 275.8
23:38:17.006 INFO ProgressMeter - chr7:13965524 54.1 14890 275.4
23:38:28.620 INFO ProgressMeter - chr7:13971386 54.3 14930 275.1
23:38:45.020 INFO ProgressMeter - chr7:13975515 54.5 14960 274.3
23:38:56.513 INFO ProgressMeter - chr7:13979430 54.7 14990 273.9
23:39:06.713 INFO ProgressMeter - chr7:13982476 54.9 15020 273.6
23:39:18.221 INFO ProgressMeter - chr7:13988084 55.1 15050 273.2
23:39:30.064 INFO ProgressMeter - chr7:13989561 55.3 15060 272.4
23:39:40.983 INFO ProgressMeter - chr7:55152674 55.5 15110 272.4
23:39:51.122 INFO ProgressMeter - chr7:55165631 55.6 15150 272.3
23:40:02.616 INFO ProgressMeter - chr7:55169231 55.8 15170 271.7
23:40:15.824 INFO ProgressMeter - chr7:55177852 56.1 15210 271.3
23:40:26.178 INFO ProgressMeter - chr7:55181333 56.2 15240 271.0
23:40:36.420 INFO ProgressMeter - chr7:78135019 56.4 15280 270.9
23:40:46.901 INFO ProgressMeter - chr7:81762790 56.6 15330 271.0
23:40:57.091 INFO ProgressMeter - chr7:92706436 56.7 15370 270.9
23:41:08.526 INFO ProgressMeter - chr7:102201408 56.9 15420 270.8
23:41:21.107 INFO ProgressMeter - chr7:106872535 57.1 15470 270.7
23:41:32.410 INFO ProgressMeter - chr7:116767501 57.3 15520 270.7
23:41:43.207 INFO ProgressMeter - chr7:137344970 57.5 15570 270.7
23:41:55.226 INFO ProgressMeter - chr7:140792609 57.7 15620 270.7
23:42:06.047 INFO ProgressMeter - chr7:140920344 57.9 15680 270.8
23:42:17.504 INFO ProgressMeter - chr7:152152703 58.1 15760 271.3
23:42:28.597 INFO ProgressMeter - chr7:152177774 58.3 15800 271.2
23:42:39.845 INFO ProgressMeter - chr7:152249874 58.5 15860 271.3
23:42:50.715 INFO ProgressMeter - chr8:32220130 58.6 15940 271.8
23:43:01.228 INFO ProgressMeter - chr8:32754370 58.8 15990 271.9
23:43:11.690 INFO ProgressMeter - chr8:38415868 59.0 16060 272.3
23:43:24.262 INFO ProgressMeter - chr8:41934446 59.2 16120 272.3
23:43:34.731 INFO ProgressMeter - chr8:47798235 59.4 16170 272.4
23:43:45.529 INFO ProgressMeter - chr8:47885942 59.6 16220 272.4
23:43:55.853 INFO ProgressMeter - chr8:55947616 59.7 16280 272.6
23:44:07.100 INFO ProgressMeter - chr8:68120919 59.9 16340 272.7
23:44:17.142 INFO ProgressMeter - chr8:92075963 60.1 16400 273.0
23:44:28.362 INFO ProgressMeter - chr8:127737555 60.3 16440 272.8
23:44:40.447 INFO ProgressMeter - chr8:144512964 60.5 16500 272.9
23:44:51.548 INFO ProgressMeter - chr9:5089672 60.7 16570 273.2
23:45:01.936 INFO ProgressMeter - chr9:8633355 60.8 16650 273.7
23:45:12.843 INFO ProgressMeter - chr9:35075705 61.0 16710 273.9
23:45:23.895 INFO ProgressMeter - chr9:84670554 61.2 16780 274.2
23:45:34.565 INFO ProgressMeter - chr9:84745055 61.4 16810 273.9
23:45:45.119 INFO ProgressMeter - chr9:84814338 61.5 16840 273.6
23:45:55.419 INFO ProgressMeter - chr9:84863220 61.7 16860 273.2
23:46:08.091 INFO ProgressMeter - chr9:84872841 61.9 16890 272.7
23:46:18.350 INFO ProgressMeter - chr9:84948460 62.1 16920 272.5
23:46:30.292 INFO ProgressMeter - chr9:85024335 62.3 16940 271.9
23:46:41.179 INFO ProgressMeter - chr9:90874771 62.5 16970 271.6
23:46:53.633 INFO ProgressMeter - chr9:95476039 62.7 17020 271.5
23:47:03.902 INFO ProgressMeter - chr9:99147652 62.9 17070 271.6
23:47:15.826 INFO ProgressMeter - chr9:130884021 63.1 17120 271.5
23:47:26.377 INFO ProgressMeter - chr9:132905945 63.2 17160 271.4
23:47:37.728 INFO ProgressMeter - chr9:136510733 63.4 17220 271.5
23:47:47.837 INFO ProgressMeter - chrX:15803686 63.6 17290 271.9
23:47:57.981 INFO ProgressMeter - chrX:40072711 63.8 17340 272.0
23:48:08.120 INFO ProgressMeter - chrX:45110077 63.9 17400 272.2
23:48:18.743 INFO ProgressMeter - chrX:48791842 64.1 17460 272.4
23:48:31.165 INFO ProgressMeter - chrX:49035425 64.3 17500 272.1
23:48:41.499 INFO ProgressMeter - chrX:49043109 64.5 17540 272.0
23:48:52.147 INFO ProgressMeter - chrX:53383076 64.7 17600 272.2
23:49:04.891 INFO ProgressMeter - chrX:64191817 64.9 17650 272.1
23:49:16.503 INFO ProgressMeter - chrX:67686008 65.1 17700 272.0
23:49:26.718 INFO ProgressMeter - chrX:71133121 65.2 17760 272.2
23:49:37.006 INFO ProgressMeter - chrX:71397251 65.4 17810 272.3
23:49:47.525 INFO ProgressMeter - chrX:77681635 65.6 17870 272.5
23:49:58.507 INFO ProgressMeter - chrX:111173016 65.8 17940 272.8
23:50:08.981 INFO ProgressMeter - chrX:124095370 65.9 18000 273.0
23:50:20.439 INFO ProgressMeter - chrX:134413802 66.1 18050 272.9
23:50:20.819 INFO Mutect2 - 844558 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
7 read(s) filtered by: ReadLengthReadFilter
135 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
844700 total reads filtered out of 114862094 reads processed
23:50:20.819 INFO ProgressMeter - chrY:20557826 66.1 18093 273.6
23:50:20.819 INFO ProgressMeter - Traversal complete. Processed 18093 total regions in 66.1 minutes.
23:50:20.835 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.772333562000001
23:50:20.835 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 370.072233878
23:50:20.835 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 150.34 sec
23:50:20.836 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:50:20 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 66.15 minutes.
Runtime.totalMemory()=3640655872
Tool returned:
SUCCESS
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0898_tumor.bam --tumor-sample LS0898 -L TST500C_manifest.bed -O LS0898.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:50:22.139 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:50:22.228 INFO FilterMutectCalls - ------------------------------------------------------------
23:50:22.230 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:50:22.230 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:50:22.230 INFO FilterMutectCalls - Executing as ?@nf-30e9aafcd75ca1aac2cc5f53546a3786-af43f-dqxhj on Linux v6.12.88 amd64
23:50:22.230 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:50:22.230 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:50:22 PM GMT
23:50:22.231 INFO FilterMutectCalls - ------------------------------------------------------------
23:50:22.231 INFO FilterMutectCalls - ------------------------------------------------------------
23:50:22.231 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:50:22.231 INFO FilterMutectCalls - Picard Version: 3.1.1
23:50:22.231 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:50:22.232 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:50:22.232 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:50:22.232 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:50:22.232 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:50:22.232 INFO FilterMutectCalls - Deflater: IntelDeflater
23:50:22.232 INFO FilterMutectCalls - Inflater: IntelInflater
23:50:22.232 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:50:22.232 INFO FilterMutectCalls - Requester pays: disabled
23:50:22.232 INFO FilterMutectCalls - Initializing engine
23:50:22.345 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.7uY8br2qWj/LS0898.mutect2.raw.vcf.gz
23:50:22.441 INFO FilterMutectCalls - Done initializing engine
23:50:22.490 INFO ProgressMeter - Starting traversal
23:50:22.490 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:50:22.491 INFO FilterMutectCalls - Starting pass 0 through the variants
23:50:23.874 INFO FilterMutectCalls - Finished pass 0 through the variants
23:50:27.322 INFO FilterMutectCalls - Starting pass 1 through the variants
23:50:28.785 INFO FilterMutectCalls - Finished pass 1 through the variants
23:50:29.591 INFO FilterMutectCalls - Starting pass 2 through the variants
23:50:31.027 INFO FilterMutectCalls - Finished pass 2 through the variants
23:50:31.028 INFO FilterMutectCalls - Starting pass 3 through the variants
23:50:32.232 INFO FilterMutectCalls - Finished pass 3 through the variants
23:50:32.238 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:50:32.238 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:50:32.238 INFO ProgressMeter - chr4:186709486 0.2 10996 67681.6
23:50:32.238 INFO ProgressMeter - Traversal complete. Processed 10996 total variants in 0.2 minutes.
23:50:32.248 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:50:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.17 minutes.
Runtime.totalMemory()=553648128
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 LS0898.mutect2.raw.vcf.gz --stats LS0898.mutect2.raw.vcf.gz.stats -O LS0898.mutect2.filtered.vcf.gz
23:50:33.368 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:50:33.458 INFO SelectVariants - ------------------------------------------------------------
23:50:33.459 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:50:33.460 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:50:33.460 INFO SelectVariants - Executing as ?@nf-30e9aafcd75ca1aac2cc5f53546a3786-af43f-dqxhj on Linux v6.12.88 amd64
23:50:33.460 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:50:33.460 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:50:33 PM GMT
23:50:33.460 INFO SelectVariants - ------------------------------------------------------------
23:50:33.460 INFO SelectVariants - ------------------------------------------------------------
23:50:33.461 INFO SelectVariants - HTSJDK Version: 4.1.0
23:50:33.461 INFO SelectVariants - Picard Version: 3.1.1
23:50:33.461 INFO SelectVariants - Built for Spark Version: 3.5.0
23:50:33.461 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:50:33.461 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:50:33.461 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:50:33.461 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:50:33.461 INFO SelectVariants - Deflater: IntelDeflater
23:50:33.461 INFO SelectVariants - Inflater: IntelInflater
23:50:33.461 INFO SelectVariants - GCS max retries/reopens: 20
23:50:33.461 INFO SelectVariants - Requester pays: disabled
23:50:33.462 INFO SelectVariants - Initializing engine
23:50:33.564 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.7uY8br2qWj/LS0898.mutect2.filtered.vcf.gz
23:50:33.658 INFO SelectVariants - Done initializing engine
23:50:33.695 INFO ProgressMeter - Starting traversal
23:50:33.696 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:50:33.767 INFO ProgressMeter - chr6:29944568 0.0 2749 2390434.8
23:50:33.767 INFO ProgressMeter - Traversal complete. Processed 2749 total variants in 0.0 minutes.
23:50:33.777 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:50:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0898.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0898.mutect2.pass.vcf.gz