Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0919/LS0919_tumor.bam
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/df/d77ac06601b5e09139f68f31b25ad4/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0919/LS0919_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/df/d77ac06601b5e09139f68f31b25ad4/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:17.243 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
22:44:17.364 INFO Mutect2 - ------------------------------------------------------------
22:44:17.368 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:17.368 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:17.368 INFO Mutect2 - Executing as ?@nf-dfd77ac06601b5e09139f68f31b25ad4-34052-dhrzw on Linux v6.12.88 amd64
22:44:17.369 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:17.369 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:17 PM GMT
22:44:17.369 INFO Mutect2 - ------------------------------------------------------------
22:44:17.369 INFO Mutect2 - ------------------------------------------------------------
22:44:17.370 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:17.370 INFO Mutect2 - Picard Version: 3.1.1
22:44:17.371 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:17.371 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:17.372 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:17.372 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:17.372 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:17.372 INFO Mutect2 - Deflater: IntelDeflater
22:44:17.372 INFO Mutect2 - Inflater: IntelInflater
22:44:17.372 INFO Mutect2 - GCS max retries/reopens: 20
22:44:17.372 INFO Mutect2 - Requester pays: disabled
22:44:17.373 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.jneUXI9uEG/LS0919_tumor.bam.bai is older than BAM /tmp/nxf.jneUXI9uEG/LS0919_tumor.bam
22:44:17.554 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.jneUXI9uEG/af-only-gnomad.hg38.vcf.gz
22:44:17.668 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.jneUXI9uEG/TST500C_manifest.bed
22:44:17.703 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:17.732 INFO Mutect2 - Done initializing engine
22:44:17.743 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
22:44:17.744 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
22:44:17.745 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:17.745 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:17.756 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
22:44:17.765 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:17.765 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:17.765 INFO IntelPairHmm - Available threads: 384
22:44:17.765 INFO IntelPairHmm - Requested threads: 4
22:44:17.765 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:17.808 INFO ProgressMeter - Starting traversal
22:44:17.809 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:28.389 INFO ProgressMeter - chr1:11139531 0.2 80 453.7
22:44:38.465 INFO ProgressMeter - chr1:15928730 0.3 150 435.7
22:44:50.000 INFO ProgressMeter - chr1:18703092 0.5 220 410.1
22:45:00.928 INFO ProgressMeter - chr1:26766455 0.7 290 403.5
22:45:11.764 INFO ProgressMeter - chr1:39897370 0.9 380 422.6
22:45:22.048 INFO ProgressMeter - chr1:46248510 1.1 470 439.0
22:45:32.244 INFO ProgressMeter - chr1:77964644 1.2 570 459.5
22:45:43.962 INFO ProgressMeter - chr1:119916401 1.4 670 466.6
22:45:58.329 INFO ProgressMeter - chr1:156873190 1.7 760 453.6
22:46:09.069 INFO ProgressMeter - chr1:158654701 1.9 840 453.0
22:46:19.473 INFO ProgressMeter - chr1:179108445 2.0 930 458.6
22:46:29.545 INFO ProgressMeter - chr1:204519648 2.2 1030 469.1
22:46:39.682 INFO ProgressMeter - chr1:226367478 2.4 1130 477.9
22:46:51.413 INFO ProgressMeter - chr1:243502951 2.6 1210 472.6
22:47:02.688 INFO ProgressMeter - chr10:27037165 2.7 1280 465.8
22:47:13.404 INFO ProgressMeter - chr10:32037252 2.9 1360 464.7
22:47:24.207 INFO ProgressMeter - chr10:43116510 3.1 1430 460.3
22:47:35.710 INFO ProgressMeter - chr10:68600979 3.3 1500 454.8
22:47:46.533 INFO ProgressMeter - chr10:89008887 3.5 1590 457.1
22:47:57.131 INFO ProgressMeter - chr10:110590391 3.7 1680 459.6
22:48:09.332 INFO ProgressMeter - chr10:121481907 3.9 1750 453.5
22:48:20.139 INFO ProgressMeter - chr11:8230420 4.0 1830 453.1
22:48:30.715 INFO ProgressMeter - chr11:69646708 4.2 1950 462.6
22:48:42.103 INFO ProgressMeter - chr11:69769909 4.4 2030 460.9
22:48:53.276 INFO ProgressMeter - chr11:69813126 4.6 2090 455.2
22:49:04.196 INFO ProgressMeter - chr11:77325326 4.8 2160 452.5
22:49:14.547 INFO ProgressMeter - chr11:77466651 4.9 2230 450.9
22:49:26.934 INFO ProgressMeter - chr11:102324582 5.2 2300 446.4
22:49:37.805 INFO ProgressMeter - chr11:112093099 5.3 2400 450.0
22:49:48.390 INFO ProgressMeter - chr11:118505096 5.5 2470 448.3
22:49:58.418 INFO ProgressMeter - chr11:125631591 5.7 2520 443.9
22:50:09.580 INFO ProgressMeter - chr11:128460588 5.9 2580 440.1
22:50:20.474 INFO ProgressMeter - chr12:313054 6.0 2650 438.4
22:50:31.052 INFO ProgressMeter - chr12:4381183 6.2 2750 442.1
22:50:41.411 INFO ProgressMeter - chr12:6591914 6.4 2820 441.1
22:50:52.500 INFO ProgressMeter - chr12:11857765 6.6 2880 437.8
22:51:04.048 INFO ProgressMeter - chr12:11865463 6.8 2930 432.8
22:51:14.864 INFO ProgressMeter - chr12:18290853 7.0 2980 428.7
22:51:25.647 INFO ProgressMeter - chr12:45817668 7.1 3080 431.9
22:51:36.929 INFO ProgressMeter - chr12:49031994 7.3 3160 431.8
22:51:47.004 INFO ProgressMeter - chr12:49044742 7.5 3220 430.1
22:51:57.135 INFO ProgressMeter - chr12:56087087 7.7 3310 432.4
22:52:07.223 INFO ProgressMeter - chr12:57465611 7.8 3390 433.3
22:52:17.336 INFO ProgressMeter - chr12:68832434 8.0 3490 436.7
22:52:27.626 INFO ProgressMeter - chr12:114681102 8.2 3580 438.5
22:52:37.890 INFO ProgressMeter - chr12:132676544 8.3 3670 440.3
22:52:48.792 INFO ProgressMeter - chr13:26401464 8.5 3770 442.7
22:53:01.277 INFO ProgressMeter - chr13:28387867 8.7 3850 441.3
22:53:11.287 INFO ProgressMeter - chr13:32336864 8.9 3910 439.8
22:53:21.693 INFO ProgressMeter - chr13:48303911 9.1 3980 439.1
22:53:32.848 INFO ProgressMeter - chr13:102862328 9.3 4090 442.1
22:53:45.945 INFO ProgressMeter - chr14:23183219 9.5 4190 442.5
22:53:56.480 INFO ProgressMeter - chr14:65077801 9.6 4290 444.8
22:54:06.948 INFO ProgressMeter - chr14:95129470 9.8 4370 445.1
22:54:18.338 INFO ProgressMeter - chr15:34347597 10.0 4450 444.6
22:54:28.880 INFO ProgressMeter - chr15:41713149 10.2 4520 443.8
22:54:39.855 INFO ProgressMeter - chr15:49430752 10.4 4580 441.8
22:54:50.199 INFO ProgressMeter - chr15:87978087 10.5 4670 443.1
22:55:01.926 INFO ProgressMeter - chr15:90760871 10.7 4770 444.3
22:55:12.913 INFO ProgressMeter - chr15:98922146 10.9 4860 445.1
22:55:23.380 INFO ProgressMeter - chr16:2176263 11.1 4970 448.0
22:55:33.407 INFO ProgressMeter - chr16:3731266 11.3 5050 448.5
22:55:44.131 INFO ProgressMeter - chr16:11258899 11.4 5140 449.4
22:55:55.060 INFO ProgressMeter - chr16:56758536 11.6 5230 450.1
22:56:06.363 INFO ProgressMeter - chr16:72793253 11.8 5310 449.6
22:56:17.417 INFO ProgressMeter - chr16:72959761 12.0 5370 447.7
22:56:28.911 INFO ProgressMeter - chr16:89284824 12.2 5460 448.1
22:56:39.481 INFO ProgressMeter - chr17:7673699 12.4 5560 449.8
22:56:49.506 INFO ProgressMeter - chr17:16057905 12.5 5650 451.0
22:57:00.060 INFO ProgressMeter - chr17:31182506 12.7 5750 452.6
22:57:11.190 INFO ProgressMeter - chr17:39471075 12.9 5850 453.9
22:57:21.692 INFO ProgressMeter - chr17:40331397 13.1 5940 454.7
22:57:32.218 INFO ProgressMeter - chr17:42323571 13.2 6060 457.7
22:57:43.310 INFO ProgressMeter - chr17:43093487 13.4 6140 457.4
22:57:54.214 INFO ProgressMeter - chr17:43534809 13.6 6210 456.4
22:58:09.202 INFO ProgressMeter - chr17:43543343 13.9 6270 452.5
22:58:19.705 INFO ProgressMeter - chr17:58363524 14.0 6350 452.5
22:58:31.404 INFO ProgressMeter - chr17:61683973 14.2 6440 452.7
22:58:41.856 INFO ProgressMeter - chr17:75778808 14.4 6530 453.4
22:58:52.086 INFO ProgressMeter - chr18:42013440 14.6 6640 455.7
22:59:02.805 INFO ProgressMeter - chr18:57558583 14.7 6720 455.6
22:59:13.072 INFO ProgressMeter - chr19:2228173 14.9 6840 458.4
22:59:23.717 INFO ProgressMeter - chr19:7174581 15.1 6960 461.0
22:59:33.787 INFO ProgressMeter - chr19:11018955 15.3 7060 462.5
22:59:44.385 INFO ProgressMeter - chr19:15189091 15.4 7160 463.6
22:59:54.973 INFO ProgressMeter - chr19:18161052 15.6 7250 464.2
23:00:05.790 INFO ProgressMeter - chr19:35721145 15.8 7350 465.2
23:00:15.946 INFO ProgressMeter - chr19:40278925 16.0 7450 466.5
23:00:26.541 INFO ProgressMeter - chr19:42290796 16.1 7520 465.8
23:00:38.057 INFO ProgressMeter - chr19:45420858 16.3 7630 467.0
23:00:48.656 INFO ProgressMeter - chr2:15941761 16.5 7720 467.5
23:00:59.564 INFO ProgressMeter - chr2:25282050 16.7 7810 467.8
23:01:10.279 INFO ProgressMeter - chr2:29223257 16.9 7880 467.0
23:01:21.404 INFO ProgressMeter - chr2:29920596 17.1 7950 466.0
23:01:33.833 INFO ProgressMeter - chr2:47470963 17.3 8030 465.0
23:01:43.860 INFO ProgressMeter - chr2:61498752 17.4 8120 465.8
23:01:54.539 INFO ProgressMeter - chr2:108763801 17.6 8200 465.6
23:02:06.011 INFO ProgressMeter - chr2:111127375 17.8 8250 463.4
23:02:17.544 INFO ProgressMeter - chr2:113224605 18.0 8290 460.7
23:02:28.444 INFO ProgressMeter - chr2:113232230 18.2 8340 458.8
23:02:39.088 INFO ProgressMeter - chr2:127287001 18.4 8390 457.1
23:02:49.115 INFO ProgressMeter - chr2:140601586 18.5 8480 457.8
23:02:59.674 INFO ProgressMeter - chr2:172592933 18.7 8570 458.3
23:03:09.819 INFO ProgressMeter - chr2:197407996 18.9 8660 459.0
23:03:20.816 INFO ProgressMeter - chr2:214780859 19.1 8760 459.8
23:03:31.219 INFO ProgressMeter - chr2:222205301 19.2 8820 458.8
23:03:41.376 INFO ProgressMeter - chr2:222212183 19.4 8860 456.9
23:03:53.254 INFO ProgressMeter - chr2:222219211 19.6 8900 454.3
23:04:03.708 INFO ProgressMeter - chr2:241851056 19.8 8970 453.8
23:04:14.673 INFO ProgressMeter - chr20:32436665 19.9 9050 453.7
23:04:25.560 INFO ProgressMeter - chr20:42448218 20.1 9160 455.1
23:04:35.603 INFO ProgressMeter - chr20:53582811 20.3 9220 454.3
23:04:45.853 INFO ProgressMeter - chr21:38381329 20.5 9310 454.9
23:04:56.533 INFO ProgressMeter - chr21:41479265 20.6 9380 454.3
23:05:09.389 INFO ProgressMeter - chr21:41491944 20.9 9410 451.1
23:05:20.914 INFO ProgressMeter - chr21:41503491 21.1 9460 449.4
23:05:31.465 INFO ProgressMeter - chr22:20991671 21.2 9540 449.4
23:05:41.599 INFO ProgressMeter - chr22:23291720 21.4 9610 449.1
23:05:52.906 INFO ProgressMeter - chr22:29282824 21.6 9720 450.3
23:06:04.262 INFO ProgressMeter - chr22:29642200 21.8 9770 448.7
23:06:15.030 INFO ProgressMeter - chr3:10034467 22.0 9860 449.1
23:06:26.336 INFO ProgressMeter - chr3:12354607 22.1 9940 448.9
23:06:37.287 INFO ProgressMeter - chr3:12361013 22.3 9980 447.0
23:06:48.983 INFO ProgressMeter - chr3:12368481 22.5 10030 445.4
23:06:59.317 INFO ProgressMeter - chr3:12376759 22.7 10080 444.2
23:07:11.302 INFO ProgressMeter - chr3:12630648 22.9 10150 443.4
23:07:22.027 INFO ProgressMeter - chr3:47086193 23.1 10250 444.3
23:07:32.278 INFO ProgressMeter - chr3:49891756 23.2 10330 444.5
23:07:42.676 INFO ProgressMeter - chr3:52634600 23.4 10420 445.0
23:07:53.488 INFO ProgressMeter - chr3:89429104 23.6 10520 445.9
23:08:04.112 INFO ProgressMeter - chr3:136500202 23.8 10610 446.3
23:08:14.672 INFO ProgressMeter - chr3:142522726 23.9 10710 447.2
23:08:24.679 INFO ProgressMeter - chr3:179198824 24.1 10800 447.9
23:08:35.816 INFO ProgressMeter - chr3:186046315 24.3 10890 448.1
23:08:45.869 INFO ProgressMeter - chr3:189872857 24.5 10960 447.9
23:08:56.492 INFO ProgressMeter - chr4:1807227 24.6 11070 449.2
23:09:07.501 INFO ProgressMeter - chr4:54264917 24.8 11170 449.9
23:09:21.236 INFO ProgressMeter - chr4:54738686 25.1 11250 449.0
23:09:31.809 INFO ProgressMeter - chr4:80281144 25.2 11340 449.4
23:09:41.927 INFO ProgressMeter - chr4:105239014 25.4 11410 449.2
23:09:52.416 INFO ProgressMeter - chr4:122876319 25.6 11480 448.8
23:10:03.571 INFO ProgressMeter - chr4:186600196 25.8 11580 449.5
23:10:14.714 INFO ProgressMeter - chr4:186706800 25.9 11650 449.0
23:10:25.422 INFO ProgressMeter - chr5:38950310 26.1 11730 449.0
23:10:37.361 INFO ProgressMeter - chr5:56882325 26.3 11840 449.7
23:10:47.630 INFO ProgressMeter - chr5:87378394 26.5 11950 451.0
23:10:58.109 INFO ProgressMeter - chr5:112842962 26.7 12010 450.3
23:11:08.854 INFO ProgressMeter - chr5:138930539 26.9 12090 450.3
23:11:19.953 INFO ProgressMeter - chr5:150068213 27.0 12170 450.1
23:11:30.383 INFO ProgressMeter - chr5:150404562 27.2 12250 450.2
23:11:41.367 INFO ProgressMeter - chr5:177095106 27.4 12330 450.1
23:11:52.092 INFO ProgressMeter - chr5:177267560 27.6 12380 449.0
23:12:02.598 INFO ProgressMeter - chr6:395845 27.7 12480 449.8
23:12:13.139 INFO ProgressMeter - chr6:26036073 27.9 12580 450.5
23:12:24.422 INFO ProgressMeter - chr6:30703619 28.1 12640 449.7
23:12:35.329 INFO ProgressMeter - chr6:32217010 28.3 12720 449.6
23:12:45.751 INFO ProgressMeter - chr6:41957050 28.5 12820 450.4
23:12:55.931 INFO ProgressMeter - chr6:106106369 28.6 12920 451.2
23:13:08.187 INFO ProgressMeter - chr6:117322674 28.8 12980 450.1
23:13:19.250 INFO ProgressMeter - chr6:117332822 29.0 13030 448.9
23:13:30.369 INFO ProgressMeter - chr6:117340696 29.2 13070 447.5
23:13:41.320 INFO ProgressMeter - chr6:135204453 29.4 13150 447.4
23:13:51.544 INFO ProgressMeter - chr6:135209165 29.6 13180 445.8
23:14:02.079 INFO ProgressMeter - chr6:135212623 29.7 13200 443.9
23:14:12.570 INFO ProgressMeter - chr6:135215396 29.9 13220 442.0
23:14:23.441 INFO ProgressMeter - chr6:149683787 30.1 13280 441.3
23:14:33.853 INFO ProgressMeter - chr6:152098730 30.3 13350 441.1
23:14:45.388 INFO ProgressMeter - chr6:161049234 30.5 13420 440.6
23:14:56.229 INFO ProgressMeter - chr7:2934556 30.6 13520 441.2
23:15:06.624 INFO ProgressMeter - chr7:13895720 30.8 13590 441.0
23:15:16.752 INFO ProgressMeter - chr7:13933708 31.0 13630 439.9
23:15:27.993 INFO ProgressMeter - chr7:13943030 31.2 13680 438.9
23:15:39.538 INFO ProgressMeter - chr7:13949480 31.4 13720 437.5
23:15:50.924 INFO ProgressMeter - chr7:13956159 31.6 13760 436.1
23:16:02.535 INFO ProgressMeter - chr7:13964827 31.7 13810 435.0
23:16:13.661 INFO ProgressMeter - chr7:13972854 31.9 13860 434.1
23:16:24.895 INFO ProgressMeter - chr7:13977277 32.1 13890 432.5
23:16:37.278 INFO ProgressMeter - chr7:13983875 32.3 13940 431.3
23:16:51.054 INFO ProgressMeter - chr7:13989706 32.6 13970 429.1
23:17:02.788 INFO ProgressMeter - chr7:55166343 32.7 14050 429.0
23:17:14.186 INFO ProgressMeter - chr7:55175529 32.9 14090 427.8
23:17:24.239 INFO ProgressMeter - chr7:55181057 33.1 14140 427.1
23:17:34.948 INFO ProgressMeter - chr7:81744998 33.3 14230 427.5
23:17:45.914 INFO ProgressMeter - chr7:92833117 33.5 14300 427.3
23:17:56.401 INFO ProgressMeter - chr7:106905107 33.6 14390 427.7
23:18:06.515 INFO ProgressMeter - chr7:129212078 33.8 14460 427.7
23:18:18.497 INFO ProgressMeter - chr7:140797598 34.0 14520 426.9
23:18:29.166 INFO ProgressMeter - chr7:152144840 34.2 14630 427.9
23:18:39.578 INFO ProgressMeter - chr7:152199277 34.4 14690 427.5
23:18:49.944 INFO ProgressMeter - chr8:31698630 34.5 14790 428.3
23:19:00.016 INFO ProgressMeter - chr8:32756503 34.7 14850 427.9
23:19:10.499 INFO ProgressMeter - chr8:38432079 34.9 14940 428.3
23:19:21.656 INFO ProgressMeter - chr8:47799208 35.1 15020 428.4
23:19:31.777 INFO ProgressMeter - chr8:54458266 35.2 15110 428.9
23:19:41.926 INFO ProgressMeter - chr8:89953578 35.4 15200 429.4
23:19:52.627 INFO ProgressMeter - chr8:127735568 35.6 15270 429.2
23:20:03.168 INFO ProgressMeter - chr8:144517048 35.8 15350 429.3
23:20:13.623 INFO ProgressMeter - chr9:8501052 35.9 15450 430.0
23:20:23.897 INFO ProgressMeter - chr9:37033984 36.1 15540 430.5
23:20:35.486 INFO ProgressMeter - chr9:84744038 36.3 15600 429.8
23:20:47.855 INFO ProgressMeter - chr9:84861938 36.5 15640 428.5
23:20:58.984 INFO ProgressMeter - chr9:84872087 36.7 15680 427.4
23:21:10.009 INFO ProgressMeter - chr9:85022906 36.9 15730 426.6
23:21:21.067 INFO ProgressMeter - chr9:90878762 37.1 15770 425.6
23:21:31.576 INFO ProgressMeter - chr9:124119118 37.2 15860 426.0
23:21:41.740 INFO ProgressMeter - chr9:132906729 37.4 15930 425.9
23:21:51.891 INFO ProgressMeter - chrX:1198671 37.6 16030 426.7
23:22:02.196 INFO ProgressMeter - chrX:49036063 37.7 16210 429.5
23:22:12.233 INFO ProgressMeter - chrX:67569275 37.9 16350 431.3
23:22:22.623 INFO ProgressMeter - chrX:77684406 38.1 16540 434.3
23:22:32.204 INFO Mutect2 - 522478 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
0 read(s) filtered by: NotSecondaryAlignmentReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
0 read(s) filtered by: ReadLengthReadFilter
84 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
522562 total reads filtered out of 70053797 reads processed
23:22:32.205 INFO ProgressMeter - chrY:20819373 38.2 16732 437.6
23:22:32.205 INFO ProgressMeter - Traversal complete. Processed 16732 total regions in 38.2 minutes.
23:22:32.223 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.913130010000001
23:22:32.223 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 224.658677581
23:22:32.223 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 7.65 sec
23:22:32.224 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:22:32 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 38.25 minutes.
Runtime.totalMemory()=6576668672
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 LS0919_tumor.bam --tumor-sample LS0919 -L TST500C_manifest.bed -O LS0919.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:22:33.978 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
23:22:34.111 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:34.113 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:34.113 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:34.113 INFO FilterMutectCalls - Executing as ?@nf-dfd77ac06601b5e09139f68f31b25ad4-34052-dhrzw on Linux v6.12.88 amd64
23:22:34.113 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:34.114 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:22:33 PM GMT
23:22:34.114 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:34.114 INFO FilterMutectCalls - ------------------------------------------------------------
23:22:34.115 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:22:34.115 INFO FilterMutectCalls - Picard Version: 3.1.1
23:22:34.115 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:22:34.115 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:34.115 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:34.115 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:34.115 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:34.116 INFO FilterMutectCalls - Deflater: IntelDeflater
23:22:34.116 INFO FilterMutectCalls - Inflater: IntelInflater
23:22:34.116 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:22:34.116 INFO FilterMutectCalls - Requester pays: disabled
23:22:34.116 INFO FilterMutectCalls - Initializing engine
23:22:34.278 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.jneUXI9uEG/LS0919.mutect2.raw.vcf.gz
23:22:34.412 INFO FilterMutectCalls - Done initializing engine
23:22:34.480 INFO ProgressMeter - Starting traversal
23:22:34.481 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:34.482 INFO FilterMutectCalls - Starting pass 0 through the variants
23:22:35.640 INFO FilterMutectCalls - Finished pass 0 through the variants
23:22:36.062 INFO FilterMutectCalls - Starting pass 1 through the variants
23:22:37.198 INFO FilterMutectCalls - Finished pass 1 through the variants
23:22:37.333 INFO FilterMutectCalls - Starting pass 2 through the variants
23:22:38.403 INFO FilterMutectCalls - Finished pass 2 through the variants
23:22:38.406 INFO FilterMutectCalls - Starting pass 3 through the variants
23:22:39.291 INFO FilterMutectCalls - Finished pass 3 through the variants
23:22:39.300 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:22:39.300 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:22:39.301 INFO ProgressMeter - chr5:80654962 0.1 9844 122564.8
23:22:39.301 INFO ProgressMeter - Traversal complete. Processed 9844 total variants in 0.1 minutes.
23:22:39.311 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:22:39 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=335544320
Using GATK jar /gatk/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx14g -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0919.mutect2.raw.vcf.gz --stats LS0919.mutect2.raw.vcf.gz.stats -O LS0919.mutect2.filtered.vcf.gz
23:22:40.679 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
23:22:40.794 INFO SelectVariants - ------------------------------------------------------------
23:22:40.796 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:22:40.796 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:22:40.796 INFO SelectVariants - Executing as ?@nf-dfd77ac06601b5e09139f68f31b25ad4-34052-dhrzw on Linux v6.12.88 amd64
23:22:40.796 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:22:40.797 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:22:40 PM GMT
23:22:40.797 INFO SelectVariants - ------------------------------------------------------------
23:22:40.797 INFO SelectVariants - ------------------------------------------------------------
23:22:40.797 INFO SelectVariants - HTSJDK Version: 4.1.0
23:22:40.797 INFO SelectVariants - Picard Version: 3.1.1
23:22:40.797 INFO SelectVariants - Built for Spark Version: 3.5.0
23:22:40.797 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:22:40.798 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:22:40.798 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:22:40.798 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:22:40.798 INFO SelectVariants - Deflater: IntelDeflater
23:22:40.798 INFO SelectVariants - Inflater: IntelInflater
23:22:40.798 INFO SelectVariants - GCS max retries/reopens: 20
23:22:40.798 INFO SelectVariants - Requester pays: disabled
23:22:40.798 INFO SelectVariants - Initializing engine
23:22:40.958 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.jneUXI9uEG/LS0919.mutect2.filtered.vcf.gz
23:22:41.063 INFO SelectVariants - Done initializing engine
23:22:41.096 INFO ProgressMeter - Starting traversal
23:22:41.096 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:22:41.171 INFO ProgressMeter - chr7:13952559 0.0 2461 2022739.7
23:22:41.171 INFO ProgressMeter - Traversal complete. Processed 2461 total variants in 0.0 minutes.
23:22:41.182 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:22:41 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=301989888
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 LS0919.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0919.mutect2.pass.vcf.gz