Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0892/LS0892_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/d0/ed41e93a76d5de9ccd794a7b624969/.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/d0/ed41e93a76d5de9ccd794a7b624969/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0892/LS0892_tumor.bam
==> STAGING COMPLETE (10 inputs)
22:44:06.198 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
22:44:06.292 INFO Mutect2 - ------------------------------------------------------------
22:44:06.294 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:06.294 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:06.294 INFO Mutect2 - Executing as ?@nf-d0ed41e93a76d5de9ccd794a7b624969-ea176-fn68t on Linux v6.12.88 amd64
22:44:06.294 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:06.295 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:06 PM GMT
22:44:06.295 INFO Mutect2 - ------------------------------------------------------------
22:44:06.295 INFO Mutect2 - ------------------------------------------------------------
22:44:06.295 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:06.295 INFO Mutect2 - Picard Version: 3.1.1
22:44:06.296 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:06.296 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:06.296 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:06.296 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:06.296 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:06.296 INFO Mutect2 - Deflater: IntelDeflater
22:44:06.296 INFO Mutect2 - Inflater: IntelInflater
22:44:06.296 INFO Mutect2 - GCS max retries/reopens: 20
22:44:06.296 INFO Mutect2 - Requester pays: disabled
22:44:06.297 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.mf3sQs3wG9/LS0892_tumor.bam.bai is older than BAM /tmp/nxf.mf3sQs3wG9/LS0892_tumor.bam
22:44:06.436 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.mf3sQs3wG9/af-only-gnomad.hg38.vcf.gz
22:44:06.550 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.mf3sQs3wG9/TST500C_manifest.bed
22:44:06.582 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:06.609 INFO Mutect2 - Done initializing engine
22:44:06.618 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
22:44:06.619 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
22:44:06.620 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:06.620 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:06.629 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
22:44:06.637 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:06.637 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:06.638 INFO IntelPairHmm - Available threads: 384
22:44:06.638 INFO IntelPairHmm - Requested threads: 4
22:44:06.638 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:06.676 INFO ProgressMeter - Starting traversal
22:44:06.677 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:16.808 INFO ProgressMeter - chr1:9724274 0.2 60 355.4
22:44:27.762 INFO ProgressMeter - chr1:11256123 0.4 140 398.4
22:44:39.000 INFO ProgressMeter - chr1:15932576 0.5 210 389.8
22:44:49.949 INFO ProgressMeter - chr1:18744812 0.7 280 388.2
22:45:00.104 INFO ProgressMeter - chr1:26760854 0.9 340 381.8
22:45:10.967 INFO ProgressMeter - chr1:36473762 1.1 420 392.0
22:45:21.203 INFO ProgressMeter - chr1:43339478 1.2 490 394.5
22:45:31.893 INFO ProgressMeter - chr1:58779729 1.4 590 415.4
22:45:41.931 INFO ProgressMeter - chr1:85274318 1.6 690 434.6
22:45:53.478 INFO ProgressMeter - chr1:119919310 1.8 780 438.2
22:46:06.283 INFO ProgressMeter - chr1:156873438 2.0 880 441.4
22:46:17.004 INFO ProgressMeter - chr1:161356678 2.2 980 451.2
22:46:27.130 INFO ProgressMeter - chr1:204525148 2.3 1140 487.0
22:46:37.647 INFO ProgressMeter - chr1:243501720 2.5 1290 512.7
22:46:48.506 INFO ProgressMeter - chr10:27060324 2.7 1390 515.4
22:46:58.972 INFO ProgressMeter - chr10:43111450 2.9 1490 518.9
22:47:10.454 INFO ProgressMeter - chr10:43117847 3.1 1540 502.8
22:47:22.179 INFO ProgressMeter - chr10:68645882 3.3 1610 494.1
22:47:32.581 INFO ProgressMeter - chr10:89014117 3.4 1720 501.2
22:47:43.419 INFO ProgressMeter - chr10:110601616 3.6 1820 503.8
22:47:55.050 INFO ProgressMeter - chr10:121483721 3.8 1900 499.2
22:48:05.725 INFO ProgressMeter - chr11:64361132 4.0 2030 509.5
22:48:18.774 INFO ProgressMeter - chr11:69647623 4.2 2120 504.6
22:48:30.678 INFO ProgressMeter - chr11:69698436 4.4 2160 490.9
22:48:47.532 INFO ProgressMeter - chr11:69702908 4.7 2190 467.9
22:48:59.564 INFO ProgressMeter - chr11:69773307 4.9 2230 456.8
22:49:10.822 INFO ProgressMeter - chr11:69777410 5.1 2260 445.8
22:49:24.782 INFO ProgressMeter - chr11:69809467 5.3 2270 428.2
22:49:37.019 INFO ProgressMeter - chr11:69817054 5.5 2300 417.8
22:49:47.204 INFO ProgressMeter - chr11:77325326 5.7 2360 415.8
22:49:57.985 INFO ProgressMeter - chr11:101128307 5.9 2480 423.6
22:50:08.109 INFO ProgressMeter - chr11:108307895 6.0 2560 425.0
22:50:18.939 INFO ProgressMeter - chr11:118503600 6.2 2670 430.3
22:50:29.118 INFO ProgressMeter - chr11:125637165 6.4 2740 429.9
22:50:40.351 INFO ProgressMeter - chr11:128489386 6.6 2810 428.3
22:50:50.604 INFO ProgressMeter - chr12:310883 6.7 2870 426.3
22:51:01.213 INFO ProgressMeter - chr12:4430742 6.9 2980 431.3
22:51:11.777 INFO ProgressMeter - chr12:6592694 7.1 3060 431.9
22:51:22.724 INFO ProgressMeter - chr12:11857735 7.3 3130 430.7
22:51:33.428 INFO ProgressMeter - chr12:11864168 7.4 3180 427.1
22:51:43.609 INFO ProgressMeter - chr12:18282080 7.6 3240 425.4
22:51:54.619 INFO ProgressMeter - chr12:45839327 7.8 3360 430.8
22:52:07.020 INFO ProgressMeter - chr12:49032158 8.0 3430 428.4
22:52:17.614 INFO ProgressMeter - chr12:49040487 8.2 3470 424.1
22:52:28.582 INFO ProgressMeter - chr12:49054526 8.4 3540 423.2
22:52:38.744 INFO ProgressMeter - chr12:56098757 8.5 3630 425.3
22:52:48.880 INFO ProgressMeter - chr12:57748124 8.7 3720 427.4
22:52:59.534 INFO ProgressMeter - chr12:94282111 8.9 3830 431.3
22:53:10.403 INFO ProgressMeter - chr12:132643835 9.1 3950 435.9
22:53:21.177 INFO ProgressMeter - chr13:21681040 9.2 4040 437.2
22:53:34.163 INFO ProgressMeter - chr13:28368582 9.5 4150 438.8
22:53:44.651 INFO ProgressMeter - chr13:32332555 9.6 4220 438.1
22:53:55.132 INFO ProgressMeter - chr13:72768783 9.8 4350 443.5
22:54:05.550 INFO ProgressMeter - chr13:109762154 10.0 4460 446.8
22:54:15.811 INFO ProgressMeter - chr14:36521796 10.2 4560 449.2
22:54:25.858 INFO ProgressMeter - chr14:68497424 10.3 4670 452.5
22:54:36.860 INFO ProgressMeter - chr14:102083032 10.5 4750 452.2
22:54:47.637 INFO ProgressMeter - chr15:34357181 10.7 4840 453.1
22:54:58.164 INFO ProgressMeter - chr15:41762223 10.9 4930 454.0
22:55:08.462 INFO ProgressMeter - chr15:87979315 11.0 5060 458.8
22:55:18.473 INFO ProgressMeter - chr15:92978337 11.2 5220 466.2
22:55:28.609 INFO ProgressMeter - chr16:2538111 11.4 5370 472.5
22:55:39.228 INFO ProgressMeter - chr16:9763965 11.5 5500 476.5
22:55:49.574 INFO ProgressMeter - chr16:23635758 11.7 5590 477.2
22:56:00.213 INFO ProgressMeter - chr16:68737414 11.9 5700 479.3
22:56:10.485 INFO ProgressMeter - chr16:72797550 12.1 5770 478.3
22:56:20.607 INFO ProgressMeter - chr16:89268476 12.2 5860 479.1
22:56:31.208 INFO ProgressMeter - chr16:89775740 12.4 5950 479.5
22:56:41.295 INFO ProgressMeter - chr17:16039431 12.6 6100 485.0
22:56:51.788 INFO ProgressMeter - chr17:31937361 12.8 6270 491.7
22:57:01.844 INFO ProgressMeter - chr17:39719789 12.9 6390 494.6
22:57:12.296 INFO ProgressMeter - chr17:42323258 13.1 6530 498.7
22:57:22.408 INFO ProgressMeter - chr17:43093931 13.3 6620 499.2
22:57:32.474 INFO ProgressMeter - chr17:43536497 13.4 6700 498.9
22:57:43.081 INFO ProgressMeter - chr17:45264737 13.6 6770 497.5
22:57:53.173 INFO ProgressMeter - chr17:59896882 13.8 6870 498.7
22:58:03.341 INFO ProgressMeter - chr17:61857056 13.9 6980 500.6
22:58:13.971 INFO ProgressMeter - chr17:80964260 14.1 7110 503.5
22:58:24.881 INFO ProgressMeter - chr18:45063058 14.3 7210 504.1
22:58:35.033 INFO ProgressMeter - chr19:2191138 14.5 7340 507.2
22:58:45.258 INFO ProgressMeter - chr19:7119447 14.6 7490 511.5
22:58:55.794 INFO ProgressMeter - chr19:10987881 14.8 7610 513.5
22:59:06.272 INFO ProgressMeter - chr19:15188233 15.0 7730 515.6
22:59:16.724 INFO ProgressMeter - chr19:29811493 15.2 7860 518.2
22:59:27.001 INFO ProgressMeter - chr19:35733767 15.3 7980 520.3
22:59:39.128 INFO ProgressMeter - chr19:41261585 15.5 8090 520.6
22:59:49.669 INFO ProgressMeter - chr19:45413395 15.7 8220 523.0
23:00:00.015 INFO ProgressMeter - chr2:15940559 15.9 8330 524.3
23:00:11.963 INFO ProgressMeter - chr2:25743168 16.1 8440 524.6
23:00:24.582 INFO ProgressMeter - chr2:29226686 16.3 8520 522.8
23:00:34.909 INFO ProgressMeter - chr2:47403237 16.5 8620 523.4
23:00:45.590 INFO ProgressMeter - chr2:60922259 16.6 8710 523.2
23:00:55.934 INFO ProgressMeter - chr2:108772970 16.8 8840 525.5
23:01:06.325 INFO ProgressMeter - chr2:113223031 17.0 8910 524.3
23:01:17.483 INFO ProgressMeter - chr2:113232259 17.2 8980 522.7
23:01:28.071 INFO ProgressMeter - chr2:140485341 17.4 9090 523.7
23:01:38.111 INFO ProgressMeter - chr2:189867797 17.5 9240 527.3
23:01:48.997 INFO ProgressMeter - chr2:222200104 17.7 9420 532.0
23:01:59.694 INFO ProgressMeter - chr2:222211676 17.9 9500 531.2
23:02:09.948 INFO ProgressMeter - chr2:222220386 18.1 9560 529.5
23:02:20.169 INFO ProgressMeter - chr20:15144220 18.2 9670 530.6
23:02:30.289 INFO ProgressMeter - chr20:32797270 18.4 9740 529.5
23:02:40.928 INFO ProgressMeter - chr20:47627000 18.6 9850 530.4
23:02:52.369 INFO ProgressMeter - chr20:58840782 18.8 9930 529.3
23:03:03.292 INFO ProgressMeter - chr21:38383217 18.9 10020 528.9
23:03:14.806 INFO ProgressMeter - chr21:41491759 19.1 10110 528.3
23:03:24.949 INFO ProgressMeter - chr21:41507656 19.3 10190 527.9
23:03:35.784 INFO ProgressMeter - chr22:23290364 19.5 10300 528.6
23:03:46.314 INFO ProgressMeter - chr22:28707017 19.7 10370 527.5
23:03:56.659 INFO ProgressMeter - chr22:29286400 19.8 10450 526.9
23:04:06.830 INFO ProgressMeter - chr22:41147937 20.0 10540 526.9
23:04:16.932 INFO ProgressMeter - chr3:12352076 20.2 10650 528.0
23:04:29.823 INFO ProgressMeter - chr3:12360633 20.4 10710 525.4
23:04:41.259 INFO ProgressMeter - chr3:12371254 20.6 10780 523.9
23:04:51.412 INFO ProgressMeter - chr3:12585930 20.7 10850 523.0
23:05:01.748 INFO ProgressMeter - chr3:37047517 20.9 10940 523.0
23:05:12.187 INFO ProgressMeter - chr3:47123201 21.1 11030 523.0
23:05:23.219 INFO ProgressMeter - chr3:52586411 21.3 11150 524.1
23:05:33.842 INFO ProgressMeter - chr3:89431148 21.5 11270 525.3
23:05:43.909 INFO ProgressMeter - chr3:138657688 21.6 11380 526.4
23:05:54.096 INFO ProgressMeter - chr3:169764908 21.8 11520 528.7
23:06:05.376 INFO ProgressMeter - chr3:186047593 22.0 11680 531.4
23:06:15.836 INFO ProgressMeter - chr4:1801365 22.2 11840 534.5
23:06:26.156 INFO ProgressMeter - chr4:54262543 22.3 11970 536.2
23:06:39.159 INFO ProgressMeter - chr4:54736496 22.5 12060 535.0
23:06:49.801 INFO ProgressMeter - chr4:80282644 22.7 12170 535.7
23:07:00.444 INFO ProgressMeter - chr4:105241325 22.9 12260 535.5
23:07:10.915 INFO ProgressMeter - chr4:186596538 23.1 12400 537.5
23:07:21.024 INFO ProgressMeter - chr5:38947262 23.2 12540 539.6
23:07:33.011 INFO ProgressMeter - chr5:56883525 23.4 12670 540.6
23:07:43.922 INFO ProgressMeter - chr5:112843130 23.6 12840 543.6
23:07:54.035 INFO ProgressMeter - chr5:142682759 23.8 12970 545.2
23:08:04.676 INFO ProgressMeter - chr5:150407150 24.0 13100 546.6
23:08:15.504 INFO ProgressMeter - chr5:177238235 24.1 13210 547.1
23:08:25.879 INFO ProgressMeter - chr6:20455963 24.3 13350 548.9
23:08:37.600 INFO ProgressMeter - chr6:29945232 24.5 13440 548.2
23:08:47.987 INFO ProgressMeter - chr6:32202074 24.7 13520 547.6
23:08:58.735 INFO ProgressMeter - chr6:41947781 24.9 13630 548.1
23:09:09.474 INFO ProgressMeter - chr6:111703997 25.0 13760 549.4
23:09:20.571 INFO ProgressMeter - chr6:117324147 25.2 13820 547.7
23:09:31.188 INFO ProgressMeter - chr6:117335599 25.4 13890 546.7
23:09:41.669 INFO ProgressMeter - chr6:117396186 25.6 13960 545.7
23:09:53.274 INFO ProgressMeter - chr6:135210706 25.8 14040 544.7
23:10:03.679 INFO ProgressMeter - chr6:137198029 26.0 14090 543.0
23:10:13.818 INFO ProgressMeter - chr6:151804265 26.1 14170 542.5
23:10:24.306 INFO ProgressMeter - chr6:157203882 26.3 14260 542.3
23:10:34.405 INFO ProgressMeter - chr6:161973300 26.5 14340 541.9
23:10:45.128 INFO ProgressMeter - chr7:13908489 26.6 14470 543.2
23:10:55.664 INFO ProgressMeter - chr7:13944733 26.8 14550 542.6
23:11:06.950 INFO ProgressMeter - chr7:13954997 27.0 14620 541.4
23:11:17.765 INFO ProgressMeter - chr7:13964156 27.2 14680 540.0
23:11:28.612 INFO ProgressMeter - chr7:13973879 27.4 14750 539.0
23:11:39.140 INFO ProgressMeter - chr7:13981433 27.5 14810 537.7
23:11:49.528 INFO ProgressMeter - chr7:50376531 27.7 14880 536.9
23:12:00.460 INFO ProgressMeter - chr7:55171026 27.9 14970 536.6
23:12:11.270 INFO ProgressMeter - chr7:78343776 28.1 15070 536.7
23:12:22.230 INFO ProgressMeter - chr7:106868494 28.3 15230 538.9
23:12:32.851 INFO ProgressMeter - chr7:140788909 28.4 15350 539.8
23:12:43.050 INFO ProgressMeter - chr7:142961793 28.6 15450 540.1
23:12:54.281 INFO ProgressMeter - chr7:152181357 28.8 15550 540.1
23:13:04.582 INFO ProgressMeter - chr8:26338888 29.0 15660 540.7
23:13:15.754 INFO ProgressMeter - chr8:32763928 29.2 15750 540.3
23:13:26.126 INFO ProgressMeter - chr8:38426456 29.3 15830 539.8
23:13:36.310 INFO ProgressMeter - chr8:47774171 29.5 15910 539.4
23:13:46.791 INFO ProgressMeter - chr8:47943851 29.7 16020 540.0
23:13:56.842 INFO ProgressMeter - chr8:89964408 29.8 16130 540.6
23:14:07.055 INFO ProgressMeter - chr8:127737044 30.0 16200 539.9
23:14:17.571 INFO ProgressMeter - chr9:5024465 30.2 16300 540.1
23:14:27.729 INFO ProgressMeter - chr9:8633362 30.4 16410 540.7
23:14:38.365 INFO ProgressMeter - chr9:83971939 30.5 16520 541.1
23:14:48.878 INFO ProgressMeter - chr9:84814338 30.7 16600 540.7
23:14:59.361 INFO ProgressMeter - chr9:84872280 30.9 16660 539.5
23:15:09.884 INFO ProgressMeter - chr9:85025271 31.1 16740 539.1
23:15:20.061 INFO ProgressMeter - chr9:130862873 31.2 16890 540.9
23:15:30.073 INFO ProgressMeter - chr9:136518643 31.4 17010 541.9
23:15:40.208 INFO ProgressMeter - chrX:45089741 31.6 17150 543.4
23:15:51.064 INFO ProgressMeter - chrX:49037071 31.7 17260 543.8
23:16:01.791 INFO ProgressMeter - chrX:64185119 31.9 17360 543.9
23:16:12.017 INFO ProgressMeter - chrX:124025838 32.1 17640 549.7
23:16:18.051 INFO Mutect2 - 396454 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
106 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
396562 total reads filtered out of 58430909 reads processed
23:16:18.052 INFO ProgressMeter - chrY:21207343 32.2 17780 552.4
23:16:18.052 INFO ProgressMeter - Traversal complete. Processed 17780 total regions in 32.2 minutes.
23:16:18.067 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.106232918
23:16:18.067 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 150.36810757400002
23:16:18.067 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 6.79 sec
23:16:18.068 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:16:18 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 32.20 minutes.
Runtime.totalMemory()=4924112896
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 LS0892_tumor.bam --tumor-sample LS0892 -L TST500C_manifest.bed -O LS0892.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:16:19.559 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
23:16:19.710 INFO FilterMutectCalls - ------------------------------------------------------------
23:16:19.713 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:16:19.713 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:16:19.713 INFO FilterMutectCalls - Executing as ?@nf-d0ed41e93a76d5de9ccd794a7b624969-ea176-fn68t on Linux v6.12.88 amd64
23:16:19.713 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:16:19.713 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:16:19 PM GMT
23:16:19.713 INFO FilterMutectCalls - ------------------------------------------------------------
23:16:19.713 INFO FilterMutectCalls - ------------------------------------------------------------
23:16:19.714 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:16:19.714 INFO FilterMutectCalls - Picard Version: 3.1.1
23:16:19.714 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:16:19.714 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:16:19.715 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:16:19.715 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:16:19.715 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:16:19.715 INFO FilterMutectCalls - Deflater: IntelDeflater
23:16:19.715 INFO FilterMutectCalls - Inflater: IntelInflater
23:16:19.715 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:16:19.715 INFO FilterMutectCalls - Requester pays: disabled
23:16:19.715 INFO FilterMutectCalls - Initializing engine
23:16:19.893 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.mf3sQs3wG9/LS0892.mutect2.raw.vcf.gz
23:16:20.009 INFO FilterMutectCalls - Done initializing engine
23:16:20.071 INFO ProgressMeter - Starting traversal
23:16:20.071 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:16:20.072 INFO FilterMutectCalls - Starting pass 0 through the variants
23:16:21.042 INFO FilterMutectCalls - Finished pass 0 through the variants
23:16:23.032 INFO FilterMutectCalls - Starting pass 1 through the variants
23:16:23.842 INFO FilterMutectCalls - Finished pass 1 through the variants
23:16:24.301 INFO FilterMutectCalls - Starting pass 2 through the variants
23:16:25.093 INFO FilterMutectCalls - Finished pass 2 through the variants
23:16:25.095 INFO FilterMutectCalls - Starting pass 3 through the variants
23:16:25.855 INFO FilterMutectCalls - Finished pass 3 through the variants
23:16:25.866 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:16:25.867 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:16:25.867 INFO ProgressMeter - chr4:54277154 0.1 9924 102732.9
23:16:25.867 INFO ProgressMeter - Traversal complete. Processed 9924 total variants in 0.1 minutes.
23:16:25.880 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:16:25 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=486539264
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 LS0892.mutect2.raw.vcf.gz --stats LS0892.mutect2.raw.vcf.gz.stats -O LS0892.mutect2.filtered.vcf.gz
23:16:27.152 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
23:16:27.255 INFO SelectVariants - ------------------------------------------------------------
23:16:27.257 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:16:27.258 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:16:27.258 INFO SelectVariants - Executing as ?@nf-d0ed41e93a76d5de9ccd794a7b624969-ea176-fn68t on Linux v6.12.88 amd64
23:16:27.258 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:16:27.258 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:16:27 PM GMT
23:16:27.258 INFO SelectVariants - ------------------------------------------------------------
23:16:27.258 INFO SelectVariants - ------------------------------------------------------------
23:16:27.259 INFO SelectVariants - HTSJDK Version: 4.1.0
23:16:27.259 INFO SelectVariants - Picard Version: 3.1.1
23:16:27.259 INFO SelectVariants - Built for Spark Version: 3.5.0
23:16:27.259 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:16:27.259 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:16:27.259 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:16:27.259 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:16:27.259 INFO SelectVariants - Deflater: IntelDeflater
23:16:27.259 INFO SelectVariants - Inflater: IntelInflater
23:16:27.259 INFO SelectVariants - GCS max retries/reopens: 20
23:16:27.259 INFO SelectVariants - Requester pays: disabled
23:16:27.260 INFO SelectVariants - Initializing engine
23:16:27.439 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.mf3sQs3wG9/LS0892.mutect2.filtered.vcf.gz
23:16:27.554 INFO SelectVariants - Done initializing engine
23:16:27.596 INFO ProgressMeter - Starting traversal
23:16:27.597 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:16:27.691 INFO ProgressMeter - chr7:13945293 0.0 2481 1635824.2
23:16:27.692 INFO ProgressMeter - Traversal complete. Processed 2481 total variants in 0.0 minutes.
23:16:27.709 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:16:27 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 LS0892.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0892.mutect2.pass.vcf.gz