Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/6b/e8189c5b8e7ab0bf6cfe88faf8a296/.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
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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/LS0883/LS0883_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/6b/e8189c5b8e7ab0bf6cfe88faf8a296/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0883/LS0883_tumor.bam
==> STAGING COMPLETE (10 inputs)
22:44:10.320 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
22:44:10.422 INFO Mutect2 - ------------------------------------------------------------
22:44:10.424 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:10.424 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:10.424 INFO Mutect2 - Executing as ?@nf-6be8189c5b8e7ab0bf6cfe88faf8a296-37515-xq9km on Linux v6.12.88 amd64
22:44:10.424 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:10.425 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:10 PM GMT
22:44:10.425 INFO Mutect2 - ------------------------------------------------------------
22:44:10.425 INFO Mutect2 - ------------------------------------------------------------
22:44:10.426 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:10.426 INFO Mutect2 - Picard Version: 3.1.1
22:44:10.426 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:10.426 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:10.426 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:10.426 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:10.426 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:10.426 INFO Mutect2 - Deflater: IntelDeflater
22:44:10.426 INFO Mutect2 - Inflater: IntelInflater
22:44:10.426 INFO Mutect2 - GCS max retries/reopens: 20
22:44:10.426 INFO Mutect2 - Requester pays: disabled
22:44:10.427 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.zHTYD6Fv5P/LS0883_tumor.bam.bai is older than BAM /tmp/nxf.zHTYD6Fv5P/LS0883_tumor.bam
22:44:10.636 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.zHTYD6Fv5P/af-only-gnomad.hg38.vcf.gz
22:44:10.749 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.zHTYD6Fv5P/TST500C_manifest.bed
22:44:10.784 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:10.812 INFO Mutect2 - Done initializing engine
22:44:10.821 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
22:44:10.823 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
22:44:10.823 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:10.824 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:10.833 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
22:44:10.842 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:10.842 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:10.842 INFO IntelPairHmm - Available threads: 384
22:44:10.842 INFO IntelPairHmm - Requested threads: 4
22:44:10.842 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:10.874 INFO ProgressMeter - Starting traversal
22:44:10.874 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:21.740 INFO ProgressMeter - chr1:11114811 0.2 70 386.6
22:44:32.950 INFO ProgressMeter - chr1:11241551 0.4 140 380.5
22:44:44.233 INFO ProgressMeter - chr1:15930332 0.6 190 341.7
22:44:56.138 INFO ProgressMeter - chr1:15935931 0.8 240 318.1
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22:45:17.899 INFO ProgressMeter - chr1:26762261 1.1 360 322.3
22:45:29.788 INFO ProgressMeter - chr1:36472236 1.3 430 326.9
22:45:40.835 INFO ProgressMeter - chr1:39902753 1.5 490 326.8
22:45:52.155 INFO ProgressMeter - chr1:46061927 1.7 560 331.8
22:46:03.019 INFO ProgressMeter - chr1:64839605 1.9 630 337.1
22:46:14.887 INFO ProgressMeter - chr1:85270785 2.1 710 343.5
22:46:27.024 INFO ProgressMeter - chr1:119514066 2.3 790 348.1
22:46:38.062 INFO ProgressMeter - chr1:119949005 2.5 840 342.4
22:46:48.336 INFO ProgressMeter - chr1:156872113 2.6 900 342.9
22:46:59.126 INFO ProgressMeter - chr1:156875080 2.8 920 328.1
22:47:10.954 INFO ProgressMeter - chr1:158638074 3.0 970 323.2
22:47:21.933 INFO ProgressMeter - chr1:158681622 3.2 1030 323.5
22:47:32.888 INFO ProgressMeter - chr1:179108158 3.4 1100 326.7
22:47:43.756 INFO ProgressMeter - chr1:204438933 3.5 1170 329.8
22:47:54.925 INFO ProgressMeter - chr1:204542459 3.7 1240 332.1
22:48:05.331 INFO ProgressMeter - chr1:206493918 3.9 1300 332.7
22:48:15.709 INFO ProgressMeter - chr1:241508601 4.1 1370 335.7
22:48:28.410 INFO ProgressMeter - chr1:243503923 4.3 1410 328.5
22:48:38.518 INFO ProgressMeter - chr10:27006896 4.5 1460 327.3
22:48:49.978 INFO ProgressMeter - chr10:27092506 4.7 1520 326.8
22:49:01.296 INFO ProgressMeter - chr10:43100558 4.8 1590 328.5
22:49:13.094 INFO ProgressMeter - chr10:43114956 5.0 1630 323.6
22:49:24.082 INFO ProgressMeter - chr10:43126113 5.2 1670 319.9
22:49:34.629 INFO ProgressMeter - chr10:68572785 5.4 1720 318.8
22:49:46.737 INFO ProgressMeter - chr10:68691760 5.6 1770 316.2
22:49:56.902 INFO ProgressMeter - chr10:89013341 5.8 1850 320.8
22:50:07.641 INFO ProgressMeter - chr10:110568917 5.9 1920 322.9
22:50:18.905 INFO ProgressMeter - chr10:113165675 6.1 1990 324.4
22:50:29.056 INFO ProgressMeter - chr10:121482937 6.3 2030 322.1
22:50:39.410 INFO ProgressMeter - chr10:121565660 6.5 2090 322.8
22:50:49.854 INFO ProgressMeter - chr11:64359234 6.6 2170 326.3
22:51:00.336 INFO ProgressMeter - chr11:69650274 6.8 2260 331.2
22:51:10.504 INFO ProgressMeter - chr11:69702708 7.0 2320 331.7
22:51:26.437 INFO ProgressMeter - chr11:69809467 7.3 2390 329.2
22:51:37.945 INFO ProgressMeter - chr11:69818232 7.5 2430 326.1
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22:51:59.408 INFO ProgressMeter - chr11:77374598 7.8 2520 322.7
22:52:09.418 INFO ProgressMeter - chr11:77423775 8.0 2550 319.7
22:52:21.135 INFO ProgressMeter - chr11:101128984 8.2 2630 321.9
22:52:32.091 INFO ProgressMeter - chr11:108229278 8.4 2670 319.6
22:52:42.261 INFO ProgressMeter - chr11:112085277 8.5 2750 322.7
22:52:53.547 INFO ProgressMeter - chr11:118482420 8.7 2800 321.4
22:53:06.485 INFO ProgressMeter - chr11:118509134 8.9 2860 320.4
22:53:17.480 INFO ProgressMeter - chr11:125629389 9.1 2900 318.3
22:53:30.805 INFO ProgressMeter - chr11:128460177 9.3 2960 317.2
22:53:41.699 INFO ProgressMeter - chr11:128810905 9.5 3020 317.4
22:53:51.964 INFO ProgressMeter - chr12:333560 9.7 3070 317.0
22:54:02.372 INFO ProgressMeter - chr12:4373398 9.9 3140 318.5
22:54:12.671 INFO ProgressMeter - chr12:4437596 10.0 3200 319.0
22:54:24.273 INFO ProgressMeter - chr12:6582135 10.2 3250 317.9
22:54:36.527 INFO ProgressMeter - chr12:11853406 10.4 3300 316.5
22:54:47.847 INFO ProgressMeter - chr12:11856978 10.6 3330 313.7
22:54:59.900 INFO ProgressMeter - chr12:11860964 10.8 3360 310.6
22:55:10.476 INFO ProgressMeter - chr12:11865752 11.0 3390 308.4
22:55:21.884 INFO ProgressMeter - chr12:11869638 11.2 3420 305.8
22:55:32.771 INFO ProgressMeter - chr12:25216711 11.4 3500 308.0
22:55:43.011 INFO ProgressMeter - chr12:45811453 11.5 3560 308.6
22:55:53.832 INFO ProgressMeter - chr12:45892009 11.7 3600 307.3
22:56:06.347 INFO ProgressMeter - chr12:49033788 11.9 3660 306.9
22:56:17.183 INFO ProgressMeter - chr12:49043361 12.1 3710 306.5
22:56:27.431 INFO ProgressMeter - chr12:50096848 12.3 3780 307.9
22:56:38.467 INFO ProgressMeter - chr12:56099689 12.5 3860 309.8
22:56:48.971 INFO ProgressMeter - chr12:57464031 12.6 3910 309.5
22:57:00.445 INFO ProgressMeter - chr12:57754586 12.8 3980 310.3
22:57:10.597 INFO ProgressMeter - chr12:68844245 13.0 4040 310.9
22:57:20.896 INFO ProgressMeter - chr12:112489022 13.2 4110 312.1
22:57:30.944 INFO ProgressMeter - chr12:132632313 13.3 4170 312.7
22:57:42.250 INFO ProgressMeter - chr12:132681164 13.5 4240 313.5
22:57:52.833 INFO ProgressMeter - chr13:21682277 13.7 4300 313.9
22:58:03.388 INFO ProgressMeter - chr13:28070489 13.9 4380 315.7
22:58:18.385 INFO ProgressMeter - chr13:28388748 14.1 4440 314.3
22:58:28.623 INFO ProgressMeter - chr13:32337789 14.3 4500 314.8
22:58:39.455 INFO ProgressMeter - chr13:32398160 14.5 4560 315.0
22:58:50.279 INFO ProgressMeter - chr13:101868723 14.7 4660 317.9
22:59:00.647 INFO ProgressMeter - chr13:102875305 14.8 4730 319.0
22:59:10.846 INFO ProgressMeter - chr13:113317499 15.0 4810 320.7
22:59:21.376 INFO ProgressMeter - chr14:37589166 15.2 4880 321.6
22:59:31.416 INFO ProgressMeter - chr14:37599303 15.3 4940 322.0
22:59:41.678 INFO ProgressMeter - chr14:95091201 15.5 5010 322.9
22:59:52.388 INFO ProgressMeter - chr14:102084876 15.7 5080 323.7
23:00:03.371 INFO ProgressMeter - chr15:34347851 15.9 5140 323.8
23:00:13.854 INFO ProgressMeter - chr15:41669673 16.0 5190 323.4
23:00:26.076 INFO ProgressMeter - chr15:41750205 16.3 5250 323.0
23:00:36.640 INFO ProgressMeter - chr15:49441215 16.4 5310 323.2
23:00:48.597 INFO ProgressMeter - chr15:87977994 16.6 5400 324.7
23:00:59.119 INFO ProgressMeter - chr15:89300298 16.8 5470 325.5
23:01:10.050 INFO ProgressMeter - chr15:92924319 17.0 5540 326.1
23:01:20.196 INFO ProgressMeter - chr15:98908804 17.2 5610 327.0
23:01:30.274 INFO ProgressMeter - chr16:2062495 17.3 5680 327.9
23:01:40.518 INFO ProgressMeter - chr16:2634495 17.5 5780 330.4
23:01:54.041 INFO ProgressMeter - chr16:3729002 17.7 5840 329.6
23:02:05.671 INFO ProgressMeter - chr16:9768849 17.9 5910 329.9
23:02:17.755 INFO ProgressMeter - chr16:23635005 18.1 5980 330.1
23:02:28.230 INFO ProgressMeter - chr16:56831840 18.3 6060 331.3
23:02:39.302 INFO ProgressMeter - chr16:72787353 18.5 6130 331.8
23:02:49.533 INFO ProgressMeter - chr16:72796522 18.6 6170 330.9
23:03:00.598 INFO ProgressMeter - chr16:72958576 18.8 6210 329.8
23:03:10.614 INFO ProgressMeter - chr16:81957954 19.0 6270 330.1
23:03:21.647 INFO ProgressMeter - chr16:89284573 19.2 6320 329.5
23:03:32.184 INFO ProgressMeter - chr17:7314078 19.4 6410 331.2
23:03:43.273 INFO ProgressMeter - chr17:7682667 19.5 6470 331.1
23:03:54.325 INFO ProgressMeter - chr17:16061562 19.7 6560 332.6
23:04:04.609 INFO ProgressMeter - chr17:17213653 19.9 6630 333.2
23:04:15.205 INFO ProgressMeter - chr17:31235685 20.1 6700 333.8
23:04:25.752 INFO ProgressMeter - chr17:35103540 20.2 6780 334.8
23:04:37.186 INFO ProgressMeter - chr17:39704947 20.4 6850 335.2
23:04:47.774 INFO ProgressMeter - chr17:40389517 20.6 6920 335.7
23:04:58.542 INFO ProgressMeter - chr17:42310623 20.8 7020 337.6
23:05:08.585 INFO ProgressMeter - chr17:43091509 21.0 7100 338.7
23:05:19.833 INFO ProgressMeter - chr17:43528303 21.1 7150 338.1
23:05:30.056 INFO ProgressMeter - chr17:43535364 21.3 7190 337.2
23:05:41.822 INFO ProgressMeter - chr17:43541714 21.5 7230 336.0
23:05:53.798 INFO ProgressMeter - chr17:45273501 21.7 7270 334.8
23:06:04.232 INFO ProgressMeter - chr17:58358015 21.9 7320 334.4
23:06:14.895 INFO ProgressMeter - chr17:59926433 22.1 7390 334.9
23:06:26.604 INFO ProgressMeter - chr17:60662993 22.3 7430 333.8
23:06:38.095 INFO ProgressMeter - chr17:65014255 22.5 7490 333.6
23:06:49.094 INFO ProgressMeter - chr17:76736159 22.6 7550 333.5
23:07:00.003 INFO ProgressMeter - chr18:751703 22.8 7630 334.4
23:07:10.810 INFO ProgressMeter - chr18:44951222 23.0 7700 334.8
23:07:21.987 INFO ProgressMeter - chr18:57558583 23.2 7760 334.7
23:07:32.060 INFO ProgressMeter - chr19:2210619 23.4 7860 336.6
23:07:42.717 INFO ProgressMeter - chr19:5218418 23.5 7960 338.3
23:07:53.368 INFO ProgressMeter - chr19:7184314 23.7 8040 339.1
23:08:04.271 INFO ProgressMeter - chr19:10491875 23.9 8110 339.5
23:08:14.288 INFO ProgressMeter - chr19:11059751 24.1 8180 340.0
23:08:25.129 INFO ProgressMeter - chr19:15174066 24.2 8240 340.0
23:08:35.405 INFO ProgressMeter - chr19:15239908 24.4 8300 340.0
23:08:46.374 INFO ProgressMeter - chr19:17844232 24.6 8370 340.4
23:08:59.590 INFO ProgressMeter - chr19:29821777 24.8 8450 340.6
23:09:10.338 INFO ProgressMeter - chr19:35732213 25.0 8530 341.3
23:09:20.913 INFO ProgressMeter - chr19:41221878 25.2 8610 342.1
23:09:31.040 INFO ProgressMeter - chr19:41878988 25.3 8650 341.4
23:09:41.062 INFO ProgressMeter - chr19:45361522 25.5 8730 342.3
23:09:52.004 INFO ProgressMeter - chr19:50402203 25.7 8820 343.4
23:10:03.433 INFO ProgressMeter - chr2:15941561 25.9 8890 343.6
23:10:14.136 INFO ProgressMeter - chr2:17781106 26.1 8950 343.5
23:10:27.073 INFO ProgressMeter - chr2:25743173 26.3 9010 343.0
23:10:40.992 INFO ProgressMeter - chr2:29222893 26.5 9070 342.2
23:10:53.643 INFO ProgressMeter - chr2:29226595 26.7 9100 340.7
23:11:04.027 INFO ProgressMeter - chr2:39345762 26.9 9150 340.3
23:11:14.872 INFO ProgressMeter - chr2:47374005 27.1 9210 340.3
23:11:26.656 INFO ProgressMeter - chr2:47799276 27.3 9260 339.7
23:11:36.735 INFO ProgressMeter - chr2:61481183 27.4 9330 340.1
23:11:46.907 INFO ProgressMeter - chr2:98535741 27.6 9380 339.8
23:11:58.606 INFO ProgressMeter - chr2:108764420 27.8 9450 340.0
23:12:09.609 INFO ProgressMeter - chr2:111126719 28.0 9510 339.9
23:12:20.969 INFO ProgressMeter - chr2:111128706 28.2 9530 338.3
23:12:31.516 INFO ProgressMeter - chr2:113222957 28.3 9570 337.6
23:12:50.359 INFO ProgressMeter - chr2:113227692 28.7 9610 335.3
23:13:02.000 INFO ProgressMeter - chr2:113231622 28.9 9650 334.5
23:13:13.596 INFO ProgressMeter - chr2:113235053 29.0 9680 333.3
23:13:23.882 INFO ProgressMeter - chr2:136119431 29.2 9740 333.4
23:13:35.538 INFO ProgressMeter - chr2:140700494 29.4 9820 333.9
23:13:46.153 INFO ProgressMeter - chr2:141810304 29.6 9890 334.3
23:13:57.165 INFO ProgressMeter - chr2:177233176 29.8 9940 333.9
23:14:07.258 INFO ProgressMeter - chr2:197400305 29.9 10010 334.3
23:14:17.752 INFO ProgressMeter - chr2:208239069 30.1 10080 334.7
23:14:29.532 INFO ProgressMeter - chr2:214792295 30.3 10160 335.2
23:14:40.644 INFO ProgressMeter - chr2:222202632 30.5 10200 334.5
23:14:52.944 INFO ProgressMeter - chr2:222207921 30.7 10240 333.5
23:15:03.429 INFO ProgressMeter - chr2:222212426 30.9 10280 332.9
23:15:17.484 INFO ProgressMeter - chr2:222216863 31.1 10320 331.7
23:15:29.005 INFO ProgressMeter - chr2:222293756 31.3 10360 331.0
23:15:40.724 INFO ProgressMeter - chr2:226797494 31.5 10420 330.8
23:15:51.556 INFO ProgressMeter - chr20:31694198 31.7 10480 330.8
23:16:03.970 INFO ProgressMeter - chr20:32436381 31.9 10530 330.3
23:16:14.538 INFO ProgressMeter - chr20:41081163 32.1 10600 330.6
23:16:25.311 INFO ProgressMeter - chr20:42791193 32.2 10670 330.9
23:16:36.803 INFO ProgressMeter - chr20:53577119 32.4 10730 330.8
23:16:48.040 INFO ProgressMeter - chr20:63700441 32.6 10800 331.1
23:17:00.466 INFO ProgressMeter - chr21:38390993 32.8 10860 330.8
23:17:11.521 INFO ProgressMeter - chr21:41473323 33.0 10910 330.5
23:17:26.138 INFO ProgressMeter - chr21:41491292 33.3 10940 329.0
23:17:37.745 INFO ProgressMeter - chr21:41498639 33.4 10980 328.3
23:17:48.623 INFO ProgressMeter - chr21:41502720 33.6 11010 327.4
23:18:00.971 INFO ProgressMeter - chr21:41507356 33.8 11050 326.6
23:18:12.059 INFO ProgressMeter - chr22:23182022 34.0 11130 327.2
23:18:22.255 INFO ProgressMeter - chr22:23310322 34.2 11170 326.7
23:18:33.177 INFO ProgressMeter - chr22:29282388 34.4 11270 327.9
23:18:43.214 INFO ProgressMeter - chr22:29298731 34.5 11310 327.5
23:18:53.777 INFO ProgressMeter - chr22:41147835 34.7 11370 327.5
23:19:06.233 INFO ProgressMeter - chr3:10060379 34.9 11450 327.9
23:19:18.226 INFO ProgressMeter - chr3:12354408 35.1 11520 328.0
23:19:32.484 INFO ProgressMeter - chr3:12360379 35.4 11560 326.9
23:19:43.813 INFO ProgressMeter - chr3:12363892 35.5 11590 326.0
23:19:54.020 INFO ProgressMeter - chr3:12369440 35.7 11630 325.6
23:20:05.763 INFO ProgressMeter - chr3:12374606 35.9 11670 324.9
23:20:16.773 INFO ProgressMeter - chr3:12433896 36.1 11720 324.7
23:20:27.184 INFO ProgressMeter - chr3:30623267 36.3 11780 324.8
23:20:38.176 INFO ProgressMeter - chr3:41235722 36.5 11860 325.3
23:20:50.402 INFO ProgressMeter - chr3:47122726 36.7 11920 325.2
23:21:00.925 INFO ProgressMeter - chr3:49895713 36.8 11990 325.5
23:21:11.207 INFO ProgressMeter - chr3:52576598 37.0 12060 325.9
23:21:22.026 INFO ProgressMeter - chr3:71000970 37.2 12140 326.5
23:21:32.936 INFO ProgressMeter - chr3:119843267 37.4 12210 326.8
23:21:43.855 INFO ProgressMeter - chr3:136340470 37.5 12270 326.8
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23:22:04.327 INFO ProgressMeter - chr3:142467932 37.9 12400 327.3
23:22:15.476 INFO ProgressMeter - chr3:169764608 38.1 12470 327.5
23:22:26.664 INFO ProgressMeter - chr3:179219947 38.3 12540 327.7
23:22:37.017 INFO ProgressMeter - chr3:185428837 38.4 12600 327.8
23:22:47.490 INFO ProgressMeter - chr3:186048464 38.6 12640 327.4
23:22:58.365 INFO ProgressMeter - chr3:189872857 38.8 12710 327.6
23:23:08.751 INFO ProgressMeter - chr3:196076098 39.0 12780 328.0
23:23:19.503 INFO ProgressMeter - chr4:20256670 39.1 12860 328.5
23:23:30.048 INFO ProgressMeter - chr4:24576550 39.3 12940 329.1
23:23:40.183 INFO ProgressMeter - chr4:54290421 39.5 13010 329.5
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23:24:03.618 INFO ProgressMeter - chr4:65602304 39.9 13130 329.2
23:24:14.772 INFO ProgressMeter - chr4:83472220 40.1 13200 329.5
23:24:26.259 INFO ProgressMeter - chr4:105241185 40.3 13260 329.4
23:24:36.469 INFO ProgressMeter - chr4:122886162 40.4 13330 329.7
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23:24:59.173 INFO ProgressMeter - chr4:186618886 40.8 13470 330.1
23:25:10.462 INFO ProgressMeter - chr4:186708422 41.0 13520 329.8
23:25:21.199 INFO ProgressMeter - chr5:38945489 41.2 13590 330.1
23:25:31.254 INFO ProgressMeter - chr5:44332026 41.3 13670 330.7
23:25:42.237 INFO ProgressMeter - chr5:58454750 41.5 13740 330.9
23:25:52.954 INFO ProgressMeter - chr5:87269250 41.7 13840 331.9
23:26:05.141 INFO ProgressMeter - chr5:112840320 41.9 13920 332.2
23:26:15.525 INFO ProgressMeter - chr5:122444561 42.1 13960 331.8
23:26:25.565 INFO ProgressMeter - chr5:138827625 42.2 14020 331.9
23:26:36.413 INFO ProgressMeter - chr5:142687587 42.4 14090 332.1
23:26:47.861 INFO ProgressMeter - chr5:150086377 42.6 14150 332.0
23:26:58.959 INFO ProgressMeter - chr5:150402401 42.8 14210 332.0
23:27:09.986 INFO ProgressMeter - chr5:177089601 43.0 14280 332.2
23:27:21.378 INFO ProgressMeter - chr5:177094506 43.2 14300 331.2
23:27:31.597 INFO ProgressMeter - chr5:177209664 43.3 14330 330.6
23:27:41.970 INFO ProgressMeter - chr5:177294116 43.5 14380 330.4
23:27:52.627 INFO ProgressMeter - chr5:180616445 43.7 14440 330.5
23:28:03.427 INFO ProgressMeter - chr6:20421020 43.9 14510 330.7
23:28:14.324 INFO ProgressMeter - chr6:26036073 44.1 14590 331.2
23:28:25.192 INFO ProgressMeter - chr6:30705195 44.2 14670 331.6
23:28:35.515 INFO ProgressMeter - chr6:32198924 44.4 14720 331.5
23:28:46.741 INFO ProgressMeter - chr6:33320009 44.6 14780 331.4
23:28:57.664 INFO ProgressMeter - chr6:41964050 44.8 14860 331.8
23:29:08.996 INFO ProgressMeter - chr6:93827465 45.0 14950 332.5
23:29:19.553 INFO ProgressMeter - chr6:117310192 45.1 15010 332.5
23:29:30.285 INFO ProgressMeter - chr6:117321788 45.3 15040 331.8
23:29:40.762 INFO ProgressMeter - chr6:117326653 45.5 15080 331.4
23:29:51.466 INFO ProgressMeter - chr6:117331453 45.7 15120 331.0
23:30:02.573 INFO ProgressMeter - chr6:117340178 45.9 15170 330.8
23:30:12.721 INFO ProgressMeter - chr6:135192322 46.0 15230 330.9
23:30:24.821 INFO ProgressMeter - chr6:135208211 46.2 15280 330.5
23:30:38.395 INFO ProgressMeter - chr6:135212608 46.5 15310 329.5
23:30:49.216 INFO ProgressMeter - chr6:135217675 46.6 15350 329.1
23:31:01.488 INFO ProgressMeter - chr6:149683984 46.8 15410 329.0
23:31:13.819 INFO ProgressMeter - chr6:151880703 47.0 15460 328.6
23:31:25.416 INFO ProgressMeter - chr6:157084753 47.2 15510 328.3
23:31:35.702 INFO ProgressMeter - chr6:161048780 47.4 15560 328.2
23:31:46.397 INFO ProgressMeter - chr6:162727660 47.6 15630 328.4
23:31:58.611 INFO ProgressMeter - chr7:13891895 47.8 15720 328.9
23:32:14.271 INFO ProgressMeter - chr7:13931602 48.1 15770 328.2
23:32:25.521 INFO ProgressMeter - chr7:13938439 48.2 15820 327.9
23:32:40.320 INFO ProgressMeter - chr7:13946062 48.5 15870 327.3
23:32:53.305 INFO ProgressMeter - chr7:13950988 48.7 15910 326.6
23:33:04.514 INFO ProgressMeter - chr7:13955421 48.9 15950 326.2
23:33:14.822 INFO ProgressMeter - chr7:13961593 49.1 15990 325.9
23:33:25.770 INFO ProgressMeter - chr7:13966850 49.2 16030 325.5
23:33:37.751 INFO ProgressMeter - chr7:13973741 49.4 16080 325.2
23:33:49.408 INFO ProgressMeter - chr7:13978457 49.6 16110 324.5
23:34:02.296 INFO ProgressMeter - chr7:13983987 49.9 16160 324.1
23:34:13.152 INFO ProgressMeter - chr7:13988885 50.0 16190 323.6
23:34:24.466 INFO ProgressMeter - chr7:55153663 50.2 16250 323.5
23:34:35.095 INFO ProgressMeter - chr7:55167310 50.4 16290 323.2
23:34:47.887 INFO ProgressMeter - chr7:55175397 50.6 16330 322.6
23:34:59.475 INFO ProgressMeter - chr7:55180029 50.8 16370 322.2
23:35:10.393 INFO ProgressMeter - chr7:55205254 51.0 16410 321.8
23:35:20.545 INFO ProgressMeter - chr7:81757183 51.2 16480 322.1
23:35:31.042 INFO ProgressMeter - chr7:101817619 51.3 16550 322.4
23:35:41.100 INFO ProgressMeter - chr7:102273345 51.5 16610 322.5
23:35:51.411 INFO ProgressMeter - chr7:116699730 51.7 16660 322.4
23:36:03.640 INFO ProgressMeter - chr7:129206197 51.9 16730 322.5
23:36:14.808 INFO ProgressMeter - chr7:140791176 52.1 16800 322.7
23:36:25.381 INFO ProgressMeter - chr7:140919192 52.2 16860 322.7
23:36:37.153 INFO ProgressMeter - chr7:152152703 52.4 16950 323.2
23:36:49.181 INFO ProgressMeter - chr7:152179832 52.6 17000 323.0
23:37:00.322 INFO ProgressMeter - chr7:152247938 52.8 17050 322.8
23:37:10.612 INFO ProgressMeter - chr8:31640127 53.0 17130 323.2
23:37:21.948 INFO ProgressMeter - chr8:32728185 53.2 17190 323.2
23:37:32.913 INFO ProgressMeter - chr8:37839497 53.4 17260 323.4
23:37:43.387 INFO ProgressMeter - chr8:38464665 53.5 17330 323.7
23:37:53.497 INFO ProgressMeter - chr8:42048750 53.7 17380 323.6
23:38:04.372 INFO ProgressMeter - chr8:47863542 53.9 17460 324.0
23:38:15.091 INFO ProgressMeter - chr8:55951964 54.1 17540 324.4
23:38:25.612 INFO ProgressMeter - chr8:89935580 54.2 17620 324.8
23:38:35.657 INFO ProgressMeter - chr8:127731368 54.4 17690 325.1
23:38:46.793 INFO ProgressMeter - chr8:144511909 54.6 17760 325.3
23:38:57.735 INFO ProgressMeter - chr9:5126331 54.8 17850 325.8
23:39:10.370 INFO ProgressMeter - chr9:20448121 55.0 17940 326.2
23:39:21.000 INFO ProgressMeter - chr9:83971651 55.2 18030 326.8
23:39:31.384 INFO ProgressMeter - chr9:84743403 55.3 18080 326.7
23:39:41.497 INFO ProgressMeter - chr9:84813874 55.5 18120 326.4
23:39:52.060 INFO ProgressMeter - chr9:84862571 55.7 18150 325.9
23:40:02.261 INFO ProgressMeter - chr9:84866745 55.9 18180 325.5
23:40:12.694 INFO ProgressMeter - chr9:84876110 56.0 18220 325.2
23:40:23.082 INFO ProgressMeter - chr9:85023629 56.2 18260 324.9
23:40:33.672 INFO ProgressMeter - chr9:90874202 56.4 18300 324.6
23:40:44.200 INFO ProgressMeter - chr9:95506405 56.6 18370 324.8
23:40:54.334 INFO ProgressMeter - chr9:130872127 56.7 18450 325.3
23:41:05.008 INFO ProgressMeter - chr9:132901587 56.9 18500 325.1
23:41:15.055 INFO ProgressMeter - chr9:136506775 57.1 18560 325.2
23:41:25.602 INFO ProgressMeter - chrX:15815675 57.2 18640 325.6
23:41:36.512 INFO ProgressMeter - chrX:45069577 57.4 18720 326.0
23:41:48.373 INFO ProgressMeter - chrX:48794126 57.6 18810 326.4
23:41:59.235 INFO ProgressMeter - chrX:49037401 57.8 18860 326.3
23:42:09.708 INFO ProgressMeter - chrX:53214687 58.0 18920 326.3
23:42:20.297 INFO ProgressMeter - chrX:53414960 58.2 18980 326.4
23:42:32.216 INFO ProgressMeter - chrX:67546209 58.4 19020 325.9
23:42:42.515 INFO ProgressMeter - chrX:71123592 58.5 19090 326.2
23:42:52.683 INFO ProgressMeter - chrX:71368052 58.7 19140 326.1
23:43:02.932 INFO ProgressMeter - chrX:77557449 58.9 19190 326.0
23:43:14.367 INFO ProgressMeter - chrX:77683984 59.1 19240 325.8
23:43:24.778 INFO ProgressMeter - chrX:123888617 59.2 19310 326.0
23:43:36.429 INFO ProgressMeter - chrX:130020983 59.4 19390 326.3
23:43:40.794 INFO Mutect2 - 679115 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
4 read(s) filtered by: ReadLengthReadFilter
157 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
679276 total reads filtered out of 98035810 reads processed
23:43:40.794 INFO ProgressMeter - chrY:20819373 59.5 19462 327.1
23:43:40.794 INFO ProgressMeter - Traversal complete. Processed 19462 total regions in 59.5 minutes.
23:43:40.810 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 7.146719485
23:43:40.810 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 299.623552822
23:43:40.810 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 11.19 sec
23:43:40.811 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:43:40 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 59.51 minutes.
Runtime.totalMemory()=5905580032
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 LS0883_tumor.bam --tumor-sample LS0883 -L TST500C_manifest.bed -O LS0883.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:43:42.375 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
23:43:42.472 INFO FilterMutectCalls - ------------------------------------------------------------
23:43:42.474 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:43:42.474 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:43:42.474 INFO FilterMutectCalls - Executing as ?@nf-6be8189c5b8e7ab0bf6cfe88faf8a296-37515-xq9km on Linux v6.12.88 amd64
23:43:42.474 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:43:42.474 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:43:42 PM GMT
23:43:42.475 INFO FilterMutectCalls - ------------------------------------------------------------
23:43:42.475 INFO FilterMutectCalls - ------------------------------------------------------------
23:43:42.475 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:43:42.475 INFO FilterMutectCalls - Picard Version: 3.1.1
23:43:42.476 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:43:42.476 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:43:42.476 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:43:42.476 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:43:42.476 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:43:42.476 INFO FilterMutectCalls - Deflater: IntelDeflater
23:43:42.476 INFO FilterMutectCalls - Inflater: IntelInflater
23:43:42.476 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:43:42.476 INFO FilterMutectCalls - Requester pays: disabled
23:43:42.477 INFO FilterMutectCalls - Initializing engine
23:43:42.640 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.zHTYD6Fv5P/LS0883.mutect2.raw.vcf.gz
23:43:42.740 INFO FilterMutectCalls - Done initializing engine
23:43:42.790 INFO ProgressMeter - Starting traversal
23:43:42.790 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:43:42.791 INFO FilterMutectCalls - Starting pass 0 through the variants
23:43:44.116 INFO FilterMutectCalls - Finished pass 0 through the variants
23:43:48.445 INFO FilterMutectCalls - Starting pass 1 through the variants
23:43:49.964 INFO FilterMutectCalls - Finished pass 1 through the variants
23:43:50.854 INFO FilterMutectCalls - Starting pass 2 through the variants
23:43:52.403 INFO FilterMutectCalls - Finished pass 2 through the variants
23:43:52.404 INFO FilterMutectCalls - Starting pass 3 through the variants
23:43:53.123 INFO ProgressMeter - chr2:113227593 0.2 9000 52269.9
23:43:53.821 INFO FilterMutectCalls - Finished pass 3 through the variants
23:43:53.827 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:43:53.828 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:43:53.828 INFO ProgressMeter - chr7:13985242 0.2 10424 56662.4
23:43:53.828 INFO ProgressMeter - Traversal complete. Processed 10424 total variants in 0.2 minutes.
23:43:53.838 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:43:53 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.19 minutes.
Runtime.totalMemory()=469762048
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 LS0883.mutect2.raw.vcf.gz --stats LS0883.mutect2.raw.vcf.gz.stats -O LS0883.mutect2.filtered.vcf.gz
23:43:55.060 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
23:43:55.176 INFO SelectVariants - ------------------------------------------------------------
23:43:55.179 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:43:55.179 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:43:55.179 INFO SelectVariants - Executing as ?@nf-6be8189c5b8e7ab0bf6cfe88faf8a296-37515-xq9km on Linux v6.12.88 amd64
23:43:55.179 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:43:55.179 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:43:55 PM GMT
23:43:55.179 INFO SelectVariants - ------------------------------------------------------------
23:43:55.180 INFO SelectVariants - ------------------------------------------------------------
23:43:55.180 INFO SelectVariants - HTSJDK Version: 4.1.0
23:43:55.180 INFO SelectVariants - Picard Version: 3.1.1
23:43:55.180 INFO SelectVariants - Built for Spark Version: 3.5.0
23:43:55.180 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:43:55.180 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:43:55.181 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:43:55.181 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:43:55.181 INFO SelectVariants - Deflater: IntelDeflater
23:43:55.181 INFO SelectVariants - Inflater: IntelInflater
23:43:55.181 INFO SelectVariants - GCS max retries/reopens: 20
23:43:55.181 INFO SelectVariants - Requester pays: disabled
23:43:55.181 INFO SelectVariants - Initializing engine
23:43:55.362 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.zHTYD6Fv5P/LS0883.mutect2.filtered.vcf.gz
23:43:55.467 INFO SelectVariants - Done initializing engine
23:43:55.503 INFO ProgressMeter - Starting traversal
23:43:55.503 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:43:55.575 INFO ProgressMeter - chr6:156778178 0.0 2606 2233714.3
23:43:55.575 INFO ProgressMeter - Traversal complete. Processed 2606 total variants in 0.0 minutes.
23:43:55.585 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:43:55 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 LS0883.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0883.mutect2.pass.vcf.gz