Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/7c/3511740a2e236449cd7422b848a5cc/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0904/LS0904_tumor.bam
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0904/LS0904_tumor.bam.bai
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/7c/3511740a2e236449cd7422b848a5cc/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:25.481 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
22:44:25.600 INFO Mutect2 - ------------------------------------------------------------
22:44:25.603 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:25.603 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:25.603 INFO Mutect2 - Executing as ?@nf-7c3511740a2e236449cd7422b848a5cc-52119-fn5j7 on Linux v6.12.88 amd64
22:44:25.603 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:25.604 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:25 PM GMT
22:44:25.604 INFO Mutect2 - ------------------------------------------------------------
22:44:25.604 INFO Mutect2 - ------------------------------------------------------------
22:44:25.604 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:25.604 INFO Mutect2 - Picard Version: 3.1.1
22:44:25.605 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:25.605 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:25.605 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:25.605 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:25.605 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:25.605 INFO Mutect2 - Deflater: IntelDeflater
22:44:25.606 INFO Mutect2 - Inflater: IntelInflater
22:44:25.606 INFO Mutect2 - GCS max retries/reopens: 20
22:44:25.606 INFO Mutect2 - Requester pays: disabled
22:44:25.606 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.pPEhC41Gmc/LS0904_tumor.bam.bai is older than BAM /tmp/nxf.pPEhC41Gmc/LS0904_tumor.bam
22:44:25.804 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.pPEhC41Gmc/af-only-gnomad.hg38.vcf.gz
22:44:25.912 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.pPEhC41Gmc/TST500C_manifest.bed
22:44:25.948 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:25.978 INFO Mutect2 - Done initializing engine
22:44:25.988 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
22:44:25.990 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
22:44:25.991 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:25.991 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:26.001 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
22:44:26.011 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:26.011 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:26.012 INFO IntelPairHmm - Available threads: 384
22:44:26.012 INFO IntelPairHmm - Requested threads: 4
22:44:26.012 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:26.051 INFO ProgressMeter - Starting traversal
22:44:26.051 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:37.196 INFO ProgressMeter - chr1:11139389 0.2 90 484.6
22:44:47.357 INFO ProgressMeter - chr1:15928427 0.4 160 450.6
22:44:58.010 INFO ProgressMeter - chr1:18636235 0.5 230 431.8
22:45:08.640 INFO ProgressMeter - chr1:26762971 0.7 300 422.7
22:45:18.877 INFO ProgressMeter - chr1:39898701 0.9 390 443.0
22:45:29.671 INFO ProgressMeter - chr1:46272464 1.1 490 462.1
22:45:39.906 INFO ProgressMeter - chr1:77969949 1.2 590 479.3
22:45:50.117 INFO ProgressMeter - chr1:119922316 1.4 680 485.3
22:46:02.877 INFO ProgressMeter - chr1:156873622 1.6 770 477.1
22:46:13.446 INFO ProgressMeter - chr1:158666314 1.8 850 474.9
22:46:24.276 INFO ProgressMeter - chr1:179117330 2.0 950 482.1
22:46:34.956 INFO ProgressMeter - chr1:204543575 2.1 1060 493.4
22:46:45.581 INFO ProgressMeter - chr1:226390408 2.3 1150 494.5
22:46:56.517 INFO ProgressMeter - chr1:243504686 2.5 1220 486.5
22:47:06.804 INFO ProgressMeter - chr10:27082782 2.7 1310 489.0
22:47:16.952 INFO ProgressMeter - chr10:43109029 2.8 1400 491.5
22:47:27.542 INFO ProgressMeter - chr10:43118335 3.0 1460 482.7
22:47:38.055 INFO ProgressMeter - chr10:68645296 3.2 1530 478.1
22:47:48.298 INFO ProgressMeter - chr10:87957851 3.4 1620 480.6
22:47:59.001 INFO ProgressMeter - chr10:110578607 3.5 1710 481.8
22:48:10.188 INFO ProgressMeter - chr10:121481074 3.7 1790 479.2
22:48:21.262 INFO ProgressMeter - chr10:121564511 3.9 1850 471.9
22:48:31.360 INFO ProgressMeter - chr11:64809891 4.1 1970 481.8
22:48:42.220 INFO ProgressMeter - chr11:69701908 4.3 2060 482.5
22:48:53.712 INFO ProgressMeter - chr11:69809467 4.5 2130 477.5
22:49:04.660 INFO ProgressMeter - chr11:76546122 4.6 2200 473.8
22:49:14.729 INFO ProgressMeter - chr11:86257513 4.8 2280 473.9
22:49:29.244 INFO ProgressMeter - chr11:102325464 5.1 2350 465.1
22:49:40.317 INFO ProgressMeter - chr11:118472982 5.2 2460 469.7
22:49:50.363 INFO ProgressMeter - chr11:118520800 5.4 2530 468.1
22:50:00.682 INFO ProgressMeter - chr11:125660451 5.6 2610 468.0
22:50:10.705 INFO ProgressMeter - chr11:128768116 5.7 2670 464.8
22:50:21.176 INFO ProgressMeter - chr12:927143 5.9 2750 464.6
22:50:31.534 INFO ProgressMeter - chr12:4438892 6.1 2840 466.2
22:50:41.703 INFO ProgressMeter - chr12:11752498 6.3 2920 466.4
22:50:53.129 INFO ProgressMeter - chr12:11861718 6.5 2980 461.9
22:51:03.675 INFO ProgressMeter - chr12:11868923 6.6 3030 457.2
22:51:14.029 INFO ProgressMeter - chr12:25226405 6.8 3120 458.8
22:51:24.968 INFO ProgressMeter - chr12:49026806 7.0 3210 459.8
22:51:35.205 INFO ProgressMeter - chr12:49038697 7.2 3270 457.2
22:51:45.320 INFO ProgressMeter - chr12:50086619 7.3 3350 457.6
22:51:56.248 INFO ProgressMeter - chr12:57092908 7.5 3450 459.8
22:52:06.755 INFO ProgressMeter - chr12:57754537 7.7 3540 461.0
22:52:17.257 INFO ProgressMeter - chr12:111447981 7.9 3640 463.5
22:52:27.739 INFO ProgressMeter - chr12:132639123 8.0 3730 464.6
22:52:37.872 INFO ProgressMeter - chr13:21045909 8.2 3820 466.0
22:52:48.263 INFO ProgressMeter - chr13:28100466 8.4 3910 467.1
22:53:01.718 INFO ProgressMeter - chr13:28399042 8.6 3970 461.9
22:53:11.832 INFO ProgressMeter - chr13:32340323 8.8 4040 461.0
22:53:22.812 INFO ProgressMeter - chr13:72768864 8.9 4140 462.8
22:53:33.593 INFO ProgressMeter - chr13:109762154 9.1 4240 464.6
22:53:44.813 INFO ProgressMeter - chr14:35402011 9.3 4320 463.9
22:53:55.089 INFO ProgressMeter - chr14:37598703 9.5 4410 465.0
22:54:06.091 INFO ProgressMeter - chr14:95106039 9.7 4500 465.5
22:54:18.651 INFO ProgressMeter - chr15:34346768 9.9 4590 464.7
22:54:29.611 INFO ProgressMeter - chr15:41710689 10.1 4660 463.3
22:54:39.757 INFO ProgressMeter - chr15:49430715 10.2 4730 462.4
22:54:51.847 INFO ProgressMeter - chr15:87978764 10.4 4830 463.1
22:55:03.330 INFO ProgressMeter - chr15:90782820 10.6 4940 465.1
22:55:13.330 INFO ProgressMeter - chr15:98923874 10.8 5030 466.3
22:55:24.000 INFO ProgressMeter - chr16:2176558 11.0 5150 469.6
22:55:34.124 INFO ProgressMeter - chr16:3757900 11.1 5250 471.5
22:55:45.138 INFO ProgressMeter - chr16:13944721 11.3 5340 471.8
22:55:56.191 INFO ProgressMeter - chr16:56834732 11.5 5440 472.9
22:56:08.001 INFO ProgressMeter - chr16:72794724 11.7 5520 471.8
22:56:18.411 INFO ProgressMeter - chr16:81869212 11.9 5580 470.0
22:56:29.396 INFO ProgressMeter - chr16:89284124 12.1 5660 469.5
22:56:39.824 INFO ProgressMeter - chr17:7674073 12.2 5770 471.8
22:56:50.432 INFO ProgressMeter - chr17:16061399 12.4 5870 473.1
22:57:01.128 INFO ProgressMeter - chr17:31222127 12.6 5970 474.4
22:57:11.531 INFO ProgressMeter - chr17:39471521 12.8 6070 475.8
22:57:21.790 INFO ProgressMeter - chr17:39728173 12.9 6150 475.7
22:57:32.179 INFO ProgressMeter - chr17:42331470 13.1 6270 478.5
22:57:42.718 INFO ProgressMeter - chr17:43104120 13.3 6350 478.2
22:57:53.332 INFO ProgressMeter - chr17:43536472 13.5 6410 476.4
22:58:06.698 INFO ProgressMeter - chr17:43543970 13.7 6460 472.3
22:58:17.451 INFO ProgressMeter - chr17:58734116 13.9 6550 472.7
22:58:28.144 INFO ProgressMeter - chr17:61686024 14.0 6640 473.1
22:58:38.218 INFO ProgressMeter - chr17:75778593 14.2 6730 473.9
22:58:48.632 INFO ProgressMeter - chr18:42033824 14.4 6840 475.8
22:58:59.424 INFO ProgressMeter - chr18:57558467 14.6 6910 474.7
22:59:09.624 INFO ProgressMeter - chr19:2222355 14.7 7030 477.4
22:59:20.313 INFO ProgressMeter - chr19:7126582 14.9 7150 479.7
22:59:30.846 INFO ProgressMeter - chr19:10986477 15.1 7250 480.8
22:59:41.394 INFO ProgressMeter - chr19:15181574 15.3 7360 482.4
22:59:51.440 INFO ProgressMeter - chr19:17841638 15.4 7460 483.7
23:00:02.412 INFO ProgressMeter - chr19:29821117 15.6 7550 483.8
23:00:13.180 INFO ProgressMeter - chr19:40240043 15.8 7660 485.3
23:00:24.330 INFO ProgressMeter - chr19:41260777 16.0 7730 484.0
23:00:35.218 INFO ProgressMeter - chr19:45364039 16.2 7830 484.7
23:00:45.399 INFO ProgressMeter - chr19:50417043 16.3 7950 487.1
23:00:56.076 INFO ProgressMeter - chr2:17766577 16.5 8030 486.7
23:01:06.857 INFO ProgressMeter - chr2:25799389 16.7 8110 486.2
23:01:19.177 INFO ProgressMeter - chr2:29226623 16.9 8180 484.4
23:01:31.319 INFO ProgressMeter - chr2:42331410 17.1 8270 484.0
23:01:41.414 INFO ProgressMeter - chr2:47800528 17.3 8330 482.7
23:01:51.614 INFO ProgressMeter - chr2:98552784 17.4 8430 483.8
23:02:02.314 INFO ProgressMeter - chr2:111125746 17.6 8520 484.0
23:02:13.013 INFO ProgressMeter - chr2:113221326 17.8 8560 481.4
23:02:23.090 INFO ProgressMeter - chr2:113226504 18.0 8600 479.1
23:02:34.092 INFO ProgressMeter - chr2:113233389 18.1 8650 477.0
23:02:44.383 INFO ProgressMeter - chr2:136112431 18.3 8710 475.8
23:02:54.719 INFO ProgressMeter - chr2:140839989 18.5 8810 476.8
23:03:05.202 INFO ProgressMeter - chr2:177234003 18.7 8900 477.1
23:03:15.629 INFO ProgressMeter - chr2:201286457 18.8 9010 478.6
23:03:26.236 INFO ProgressMeter - chr2:222200485 19.0 9100 478.9
23:03:38.164 INFO ProgressMeter - chr2:222208787 19.2 9150 476.5
23:03:49.733 INFO ProgressMeter - chr2:222217559 19.4 9200 474.4
23:04:00.324 INFO ProgressMeter - chr2:226795382 19.6 9270 473.7
23:04:11.446 INFO ProgressMeter - chr20:32433492 19.8 9360 473.8
23:04:21.915 INFO ProgressMeter - chr20:41113968 19.9 9450 474.1
23:04:32.971 INFO ProgressMeter - chr20:53576596 20.1 9540 474.3
23:04:43.593 INFO ProgressMeter - chr21:38380026 20.3 9640 475.1
23:04:53.801 INFO ProgressMeter - chr21:41468405 20.5 9700 474.0
23:05:07.119 INFO ProgressMeter - chr21:41491890 20.7 9740 470.9
23:05:18.303 INFO ProgressMeter - chr21:41501903 20.9 9790 469.1
23:05:28.837 INFO ProgressMeter - chr21:43101410 21.0 9850 468.0
23:05:42.635 INFO ProgressMeter - chr22:23292385 21.3 9950 467.7
23:05:53.693 INFO ProgressMeter - chr22:29283781 21.5 10060 468.8
23:06:04.037 INFO ProgressMeter - chr22:29300120 21.6 10100 466.9
23:06:14.773 INFO ProgressMeter - chr22:41176771 21.8 10200 467.6
23:06:25.845 INFO ProgressMeter - chr3:12352851 22.0 10290 467.8
23:06:42.009 INFO ProgressMeter - chr3:12360633 22.3 10340 464.4
23:06:56.159 INFO ProgressMeter - chr3:12370055 22.5 10400 462.2
23:07:06.188 INFO ProgressMeter - chr3:12378564 22.7 10450 461.0
23:07:17.080 INFO ProgressMeter - chr3:30688382 22.9 10530 460.8
23:07:27.159 INFO ProgressMeter - chr3:47122359 23.0 10630 461.8
23:07:37.676 INFO ProgressMeter - chr3:52550745 23.2 10730 462.6
23:07:48.404 INFO ProgressMeter - chr3:89210277 23.4 10840 463.8
23:07:59.324 INFO ProgressMeter - chr3:136433535 23.6 10940 464.5
23:08:09.364 INFO ProgressMeter - chr3:142519667 23.7 11040 465.4
23:08:20.058 INFO ProgressMeter - chr3:179232507 23.9 11150 466.5
23:08:31.569 INFO ProgressMeter - chr3:186052028 24.1 11230 466.1
23:08:41.604 INFO ProgressMeter - chr3:196076177 24.3 11340 467.5
23:08:52.871 INFO ProgressMeter - chr4:24570633 24.4 11460 468.8
23:09:06.994 INFO ProgressMeter - chr4:54731974 24.7 11560 468.4
23:09:17.932 INFO ProgressMeter - chr4:80271441 24.9 11660 468.9
23:09:28.496 INFO ProgressMeter - chr4:105238425 25.0 11750 469.2
23:09:38.752 INFO ProgressMeter - chr4:122873484 25.2 11820 468.8
23:09:48.996 INFO ProgressMeter - chr4:186601267 25.4 11920 469.6
23:09:59.765 INFO ProgressMeter - chr4:186707942 25.6 11990 469.1
23:10:10.673 INFO ProgressMeter - chr5:38950293 25.7 12070 468.9
23:10:21.341 INFO ProgressMeter - chr5:56881879 25.9 12180 469.9
23:10:31.512 INFO ProgressMeter - chr5:87346670 26.1 12290 471.0
23:10:42.281 INFO ProgressMeter - chr5:112843478 26.3 12370 470.9
23:10:52.683 INFO ProgressMeter - chr5:142627759 26.4 12460 471.2
23:11:03.151 INFO ProgressMeter - chr5:150080229 26.6 12540 471.1
23:11:13.444 INFO ProgressMeter - chr5:161692157 26.8 12630 471.4
23:11:25.799 INFO ProgressMeter - chr5:177135675 27.0 12710 470.8
23:11:35.922 INFO ProgressMeter - chr5:180608279 27.2 12790 470.8
23:11:46.082 INFO ProgressMeter - chr6:20481204 27.3 12900 471.9
23:11:56.585 INFO ProgressMeter - chr6:29944498 27.5 12980 471.8
23:12:06.596 INFO ProgressMeter - chr6:32204251 27.7 13060 471.9
23:12:17.331 INFO ProgressMeter - chr6:41969781 27.9 13170 472.8
23:12:28.026 INFO ProgressMeter - chr6:111694373 28.0 13280 473.7
23:12:40.044 INFO ProgressMeter - chr6:117322229 28.2 13340 472.5
23:12:50.233 INFO ProgressMeter - chr6:117332123 28.4 13390 471.4
23:13:00.803 INFO ProgressMeter - chr6:117352988 28.6 13450 470.6
23:13:12.151 INFO ProgressMeter - chr6:135208003 28.8 13540 470.7
23:13:25.179 INFO ProgressMeter - chr6:135212911 29.0 13570 468.2
23:13:35.917 INFO ProgressMeter - chr6:149662118 29.2 13640 467.7
23:13:46.968 INFO ProgressMeter - chr6:152098730 29.3 13720 467.5
23:13:57.064 INFO ProgressMeter - chr6:161086582 29.5 13800 467.5
23:14:07.194 INFO ProgressMeter - chr7:5978594 29.7 13900 468.2
23:14:19.473 INFO ProgressMeter - chr7:13908364 29.9 13960 467.0
23:14:30.937 INFO ProgressMeter - chr7:13936182 30.1 14000 465.4
23:14:41.838 INFO ProgressMeter - chr7:13943632 30.3 14050 464.3
23:14:53.107 INFO ProgressMeter - chr7:13949155 30.5 14090 462.7
23:15:03.610 INFO ProgressMeter - chr7:13954573 30.6 14130 461.4
23:15:15.647 INFO ProgressMeter - chr7:13961258 30.8 14170 459.7
23:15:26.625 INFO ProgressMeter - chr7:13967793 31.0 14210 458.2
23:15:38.055 INFO ProgressMeter - chr7:13974884 31.2 14260 457.1
23:15:48.178 INFO ProgressMeter - chr7:13977847 31.4 14280 455.2
23:16:01.897 INFO ProgressMeter - chr7:13984433 31.6 14330 453.5
23:16:12.787 INFO ProgressMeter - chr7:41690097 31.8 14370 452.2
23:16:23.067 INFO ProgressMeter - chr7:55161888 32.0 14440 452.0
23:16:33.556 INFO ProgressMeter - chr7:55170777 32.1 14480 450.7
23:16:44.409 INFO ProgressMeter - chr7:55198015 32.3 14530 449.8
23:16:54.787 INFO ProgressMeter - chr7:86786259 32.5 14610 449.8
23:17:04.831 INFO ProgressMeter - chr7:102234031 32.6 14700 450.3
23:17:15.269 INFO ProgressMeter - chr7:116771496 32.8 14780 450.3
23:17:26.054 INFO ProgressMeter - chr7:140789930 33.0 14860 450.3
23:17:36.475 INFO ProgressMeter - chr7:142958302 33.2 14950 450.7
23:17:46.585 INFO ProgressMeter - chr7:152174129 33.3 15040 451.1
23:17:58.593 INFO ProgressMeter - chr7:152251937 33.5 15110 450.5
23:18:11.505 INFO ProgressMeter - chr8:32647862 33.8 15220 450.9
23:18:21.558 INFO ProgressMeter - chr8:38420866 33.9 15320 451.6
23:18:32.595 INFO ProgressMeter - chr8:47776842 34.1 15400 451.5
23:18:42.782 INFO ProgressMeter - chr8:47897253 34.3 15480 451.6
23:18:53.695 INFO ProgressMeter - chr8:73946628 34.5 15590 452.4
23:19:04.198 INFO ProgressMeter - chr8:127737755 34.6 15680 452.7
23:19:14.471 INFO ProgressMeter - chr9:5024465 34.8 15770 453.1
23:19:25.435 INFO ProgressMeter - chr9:20360740 35.0 15880 453.8
23:19:36.628 INFO ProgressMeter - chr9:83974536 35.2 15980 454.3
23:19:47.163 INFO ProgressMeter - chr9:84751984 35.4 16030 453.4
23:19:58.614 INFO ProgressMeter - chr9:84862802 35.5 16080 452.4
23:20:10.567 INFO ProgressMeter - chr9:84874833 35.7 16130 451.3
23:20:21.842 INFO ProgressMeter - chr9:85024595 35.9 16180 450.3
23:20:32.024 INFO ProgressMeter - chr9:95479146 36.1 16260 450.4
23:20:42.588 INFO ProgressMeter - chr9:130885887 36.3 16350 450.7
23:20:53.280 INFO ProgressMeter - chr9:136514530 36.5 16450 451.3
23:21:03.591 INFO ProgressMeter - chrX:47571321 36.6 16640 454.3
23:21:14.161 INFO ProgressMeter - chrX:64192120 36.8 16790 456.2
23:21:24.171 INFO ProgressMeter - chrX:77652246 37.0 16980 459.3
23:21:34.214 INFO ProgressMeter - chrY:8670866 37.1 17180 462.6
23:21:34.788 INFO Mutect2 - 534118 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
2 read(s) filtered by: ReadLengthReadFilter
107 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
534227 total reads filtered out of 67306959 reads processed
23:21:34.789 INFO ProgressMeter - chrY:20960482 37.1 17211 463.3
23:21:34.789 INFO ProgressMeter - Traversal complete. Processed 17211 total regions in 37.1 minutes.
23:21:34.805 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.569540170000001
23:21:34.805 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 200.90861014400002
23:21:34.805 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 7.09 sec
23:21:34.806 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:21:34 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 37.16 minutes.
Runtime.totalMemory()=2063597568
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 LS0904_tumor.bam --tumor-sample LS0904 -L TST500C_manifest.bed -O LS0904.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:21:36.345 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
23:21:36.477 INFO FilterMutectCalls - ------------------------------------------------------------
23:21:36.479 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:21:36.479 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:21:36.479 INFO FilterMutectCalls - Executing as ?@nf-7c3511740a2e236449cd7422b848a5cc-52119-fn5j7 on Linux v6.12.88 amd64
23:21:36.479 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:21:36.479 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:21:36 PM GMT
23:21:36.480 INFO FilterMutectCalls - ------------------------------------------------------------
23:21:36.480 INFO FilterMutectCalls - ------------------------------------------------------------
23:21:36.480 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:21:36.480 INFO FilterMutectCalls - Picard Version: 3.1.1
23:21:36.480 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:21:36.480 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:21:36.480 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:21:36.481 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:21:36.481 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:21:36.481 INFO FilterMutectCalls - Deflater: IntelDeflater
23:21:36.481 INFO FilterMutectCalls - Inflater: IntelInflater
23:21:36.481 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:21:36.481 INFO FilterMutectCalls - Requester pays: disabled
23:21:36.481 INFO FilterMutectCalls - Initializing engine
23:21:36.629 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.pPEhC41Gmc/LS0904.mutect2.raw.vcf.gz
23:21:36.745 INFO FilterMutectCalls - Done initializing engine
23:21:36.803 INFO ProgressMeter - Starting traversal
23:21:36.804 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:21:36.805 INFO FilterMutectCalls - Starting pass 0 through the variants
23:21:38.055 INFO FilterMutectCalls - Finished pass 0 through the variants
23:21:38.697 INFO FilterMutectCalls - Starting pass 1 through the variants
23:21:39.869 INFO FilterMutectCalls - Finished pass 1 through the variants
23:21:40.040 INFO FilterMutectCalls - Starting pass 2 through the variants
23:21:41.134 INFO FilterMutectCalls - Finished pass 2 through the variants
23:21:41.137 INFO FilterMutectCalls - Starting pass 3 through the variants
23:21:42.114 INFO FilterMutectCalls - Finished pass 3 through the variants
23:21:42.123 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:21:42.123 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:21:42.123 INFO ProgressMeter - chr6:29943421 0.1 9688 109283.7
23:21:42.124 INFO ProgressMeter - Traversal complete. Processed 9688 total variants in 0.1 minutes.
23:21:42.137 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:21:42 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=327155712
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 LS0904.mutect2.raw.vcf.gz --stats LS0904.mutect2.raw.vcf.gz.stats -O LS0904.mutect2.filtered.vcf.gz
23:21:43.421 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
23:21:43.524 INFO SelectVariants - ------------------------------------------------------------
23:21:43.527 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:21:43.527 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:21:43.527 INFO SelectVariants - Executing as ?@nf-7c3511740a2e236449cd7422b848a5cc-52119-fn5j7 on Linux v6.12.88 amd64
23:21:43.528 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:21:43.528 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:21:43 PM GMT
23:21:43.528 INFO SelectVariants - ------------------------------------------------------------
23:21:43.528 INFO SelectVariants - ------------------------------------------------------------
23:21:43.528 INFO SelectVariants - HTSJDK Version: 4.1.0
23:21:43.528 INFO SelectVariants - Picard Version: 3.1.1
23:21:43.529 INFO SelectVariants - Built for Spark Version: 3.5.0
23:21:43.529 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:21:43.529 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:21:43.529 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:21:43.529 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:21:43.529 INFO SelectVariants - Deflater: IntelDeflater
23:21:43.529 INFO SelectVariants - Inflater: IntelInflater
23:21:43.529 INFO SelectVariants - GCS max retries/reopens: 20
23:21:43.529 INFO SelectVariants - Requester pays: disabled
23:21:43.530 INFO SelectVariants - Initializing engine
23:21:43.689 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.pPEhC41Gmc/LS0904.mutect2.filtered.vcf.gz
23:21:43.808 INFO SelectVariants - Done initializing engine
23:21:43.844 INFO ProgressMeter - Starting traversal
23:21:43.845 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:21:43.911 INFO ProgressMeter - chr7:13970100 0.0 2422 2270625.0
23:21:43.911 INFO ProgressMeter - Traversal complete. Processed 2422 total variants in 0.0 minutes.
23:21:43.921 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:21:43 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=352321536
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 LS0904.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0904.mutect2.pass.vcf.gz