Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/3d/2d0aed8b32a32f069823bdaf9bf383/.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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0921/LS0921_tumor.bam
Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.dict
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/3d/2d0aed8b32a32f069823bdaf9bf383/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0921/LS0921_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:11.056 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
22:44:11.158 INFO Mutect2 - ------------------------------------------------------------
22:44:11.160 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:11.160 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:11.160 INFO Mutect2 - Executing as ?@nf-3d2d0aed8b32a32f069823bdaf9bf383-988fd-w28vz on Linux v6.12.88 amd64
22:44:11.160 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:11.160 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:11 PM GMT
22:44:11.160 INFO Mutect2 - ------------------------------------------------------------
22:44:11.160 INFO Mutect2 - ------------------------------------------------------------
22:44:11.161 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:11.161 INFO Mutect2 - Picard Version: 3.1.1
22:44:11.161 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:11.162 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:11.162 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:11.162 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:11.162 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:11.162 INFO Mutect2 - Deflater: IntelDeflater
22:44:11.162 INFO Mutect2 - Inflater: IntelInflater
22:44:11.162 INFO Mutect2 - GCS max retries/reopens: 20
22:44:11.162 INFO Mutect2 - Requester pays: disabled
22:44:11.163 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.KmgEqbjZlB/LS0921_tumor.bam.bai is older than BAM /tmp/nxf.KmgEqbjZlB/LS0921_tumor.bam
22:44:11.344 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.KmgEqbjZlB/af-only-gnomad.hg38.vcf.gz
22:44:11.466 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.KmgEqbjZlB/TST500C_manifest.bed
22:44:11.503 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:11.534 INFO Mutect2 - Done initializing engine
22:44:11.548 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
22:44:11.550 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
22:44:11.551 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:11.551 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:11.563 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
22:44:11.572 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:11.572 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:11.572 INFO IntelPairHmm - Available threads: 384
22:44:11.572 INFO IntelPairHmm - Requested threads: 4
22:44:11.572 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:11.617 INFO ProgressMeter - Starting traversal
22:44:11.617 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:21.802 INFO ProgressMeter - chr1:11146674 0.2 100 589.2
22:44:32.251 INFO ProgressMeter - chr1:15930465 0.3 190 552.5
22:44:43.105 INFO ProgressMeter - chr1:18744812 0.5 290 552.6
22:44:53.276 INFO ProgressMeter - chr1:26779064 0.7 380 547.3
22:45:03.432 INFO ProgressMeter - chr1:43340106 0.9 510 590.6
22:45:14.039 INFO ProgressMeter - chr1:64873368 1.0 650 624.8
22:45:24.453 INFO ProgressMeter - chr1:119514331 1.2 780 642.5
22:45:34.543 INFO ProgressMeter - chr1:156872764 1.4 890 644.0
22:45:45.011 INFO ProgressMeter - chr1:158666314 1.6 990 636.0
22:45:55.528 INFO ProgressMeter - chr1:204424850 1.7 1140 658.3
22:46:05.964 INFO ProgressMeter - chr1:226065654 1.9 1280 671.6
22:46:18.124 INFO ProgressMeter - chr1:243504447 2.1 1380 654.5
22:46:28.816 INFO ProgressMeter - chr10:32010515 2.3 1500 656.0
22:46:39.083 INFO ProgressMeter - chr10:43115785 2.5 1600 651.0
22:46:50.315 INFO ProgressMeter - chr10:68573777 2.6 1690 639.0
22:47:02.894 INFO ProgressMeter - chr10:101770444 2.9 1830 641.1
22:47:13.305 INFO ProgressMeter - chr10:110602453 3.0 1950 644.0
22:47:23.362 INFO ProgressMeter - chr10:121515115 3.2 2040 638.4
22:47:33.650 INFO ProgressMeter - chr11:64369444 3.4 2170 644.5
22:47:44.319 INFO ProgressMeter - chr11:69701530 3.5 2300 648.8
22:47:56.320 INFO ProgressMeter - chr11:69810603 3.7 2390 638.2
22:48:06.681 INFO ProgressMeter - chr11:77349174 3.9 2480 633.0
22:48:17.459 INFO ProgressMeter - chr11:102229809 4.1 2620 639.4
22:48:27.634 INFO ProgressMeter - chr11:108325308 4.3 2710 635.1
22:48:38.869 INFO ProgressMeter - chr11:118505400 4.5 2830 635.4
22:48:49.176 INFO ProgressMeter - chr11:125667036 4.6 2940 635.5
22:49:00.371 INFO ProgressMeter - chr11:128811980 4.8 3030 629.6
22:49:10.708 INFO ProgressMeter - chr12:4375255 5.0 3160 633.9
22:49:20.899 INFO ProgressMeter - chr12:6593089 5.2 3280 636.3
22:49:31.541 INFO ProgressMeter - chr12:11859785 5.3 3360 630.2
22:49:43.217 INFO ProgressMeter - chr12:11868686 5.5 3440 622.4
22:49:53.743 INFO ProgressMeter - chr12:31797567 5.7 3570 626.1
22:50:04.072 INFO ProgressMeter - chr12:49032739 5.9 3670 624.8
22:50:14.625 INFO ProgressMeter - chr12:49054305 6.1 3770 623.1
22:50:25.552 INFO ProgressMeter - chr12:57094487 6.2 3910 627.4
22:50:36.129 INFO ProgressMeter - chr12:68838163 6.4 4040 630.4
22:50:46.941 INFO ProgressMeter - chr12:132634287 6.6 4180 634.4
22:50:57.569 INFO ProgressMeter - chr13:21681874 6.8 4300 635.5
22:51:08.048 INFO ProgressMeter - chr13:28368596 6.9 4430 638.3
22:51:18.562 INFO ProgressMeter - chr13:32332681 7.1 4500 632.4
22:51:28.827 INFO ProgressMeter - chr13:32398160 7.3 4590 629.9
22:51:38.946 INFO ProgressMeter - chr13:102856050 7.5 4740 635.8
22:51:50.345 INFO ProgressMeter - chr14:25381560 7.6 4860 635.7
22:52:00.642 INFO ProgressMeter - chr14:67835078 7.8 4980 637.1
22:52:11.426 INFO ProgressMeter - chr14:102101922 8.0 5100 637.8
22:52:22.264 INFO ProgressMeter - chr15:34356594 8.2 5180 633.5
22:52:33.888 INFO ProgressMeter - chr15:41766677 8.4 5280 630.7
22:52:44.796 INFO ProgressMeter - chr15:87978466 8.6 5410 632.5
22:52:55.234 INFO ProgressMeter - chr15:90784919 8.7 5550 636.0
22:53:05.984 INFO ProgressMeter - chr16:293486 8.9 5680 637.8
22:53:16.557 INFO ProgressMeter - chr16:3595603 9.1 5840 643.0
22:53:26.983 INFO ProgressMeter - chr16:9849754 9.3 5950 642.8
22:53:37.171 INFO ProgressMeter - chr16:50754317 9.4 6060 642.9
22:53:48.926 INFO ProgressMeter - chr16:72793897 9.6 6190 643.3
22:53:59.559 INFO ProgressMeter - chr16:81858261 9.8 6270 639.9
22:54:09.934 INFO ProgressMeter - chr16:89291066 10.0 6380 639.8
22:54:20.214 INFO ProgressMeter - chr17:7675051 10.1 6500 640.8
22:54:31.022 INFO ProgressMeter - chr17:16108784 10.3 6640 643.2
22:54:41.215 INFO ProgressMeter - chr17:31947615 10.5 6790 647.1
22:54:51.960 INFO ProgressMeter - chr17:39727687 10.7 6930 649.3
22:55:02.124 INFO ProgressMeter - chr17:43045688 10.8 7100 654.9
22:55:12.313 INFO ProgressMeter - chr17:43115724 11.0 7190 652.9
22:55:22.961 INFO ProgressMeter - chr17:43539558 11.2 7270 649.7
22:55:33.645 INFO ProgressMeter - chr17:45273737 11.4 7340 645.7
22:55:44.529 INFO ProgressMeter - chr17:60600413 11.5 7480 647.7
22:55:54.903 INFO ProgressMeter - chr17:68551082 11.7 7600 648.4
22:56:05.170 INFO ProgressMeter - chr18:42081121 11.9 7750 651.7
22:56:15.312 INFO ProgressMeter - chr18:59901332 12.1 7860 651.7
22:56:25.959 INFO ProgressMeter - chr19:5211639 12.2 8030 656.1
22:56:36.210 INFO ProgressMeter - chr19:10156389 12.4 8160 657.5
22:56:46.543 INFO ProgressMeter - chr19:15170669 12.6 8300 659.7
22:56:56.980 INFO ProgressMeter - chr19:17843378 12.8 8420 660.1
22:57:07.258 INFO ProgressMeter - chr19:35721723 12.9 8550 661.4
22:57:18.199 INFO ProgressMeter - chr19:41260113 13.1 8690 662.9
22:57:28.311 INFO ProgressMeter - chr19:45362673 13.3 8780 661.2
22:57:38.694 INFO ProgressMeter - chr2:9945620 13.5 8930 663.9
22:57:48.741 INFO ProgressMeter - chr2:25252243 13.6 9030 663.1
22:57:59.978 INFO ProgressMeter - chr2:29224093 13.8 9130 661.3
22:58:10.789 INFO ProgressMeter - chr2:39346086 14.0 9200 657.8
22:58:21.119 INFO ProgressMeter - chr2:47478270 14.2 9300 656.9
22:58:31.422 INFO ProgressMeter - chr2:96265136 14.3 9420 657.4
22:58:41.744 INFO ProgressMeter - chr2:111125440 14.5 9540 657.8
22:58:52.835 INFO ProgressMeter - chr2:113224271 14.7 9620 655.0
22:59:03.616 INFO ProgressMeter - chr2:113231490 14.9 9680 651.1
22:59:13.774 INFO ProgressMeter - chr2:127292806 15.0 9760 649.1
22:59:23.808 INFO ProgressMeter - chr2:140982158 15.2 9900 651.2
22:59:34.270 INFO ProgressMeter - chr2:197396054 15.4 10040 652.9
22:59:44.816 INFO ProgressMeter - chr2:214767580 15.6 10180 654.5
22:59:54.827 INFO ProgressMeter - chr2:222206057 15.7 10250 652.0
23:00:05.184 INFO ProgressMeter - chr2:222215716 15.9 10320 649.4
23:00:15.709 INFO ProgressMeter - chr2:224569687 16.1 10410 647.9
23:00:26.820 INFO ProgressMeter - chr20:32435877 16.3 10520 647.3
23:00:36.930 INFO ProgressMeter - chr20:43189687 16.4 10660 649.1
23:00:47.708 INFO ProgressMeter - chr20:58854330 16.6 10760 648.1
23:00:57.784 INFO ProgressMeter - chr21:38471027 16.8 10870 648.2
23:01:08.344 INFO ProgressMeter - chr21:41491059 16.9 10950 646.2
23:01:19.727 INFO ProgressMeter - chr21:41502289 17.1 11010 642.5
23:01:30.093 INFO ProgressMeter - chr22:20996884 17.3 11120 642.5
23:01:40.484 INFO ProgressMeter - chr22:28700068 17.5 11220 641.8
23:01:51.818 INFO ProgressMeter - chr22:29291560 17.7 11320 640.6
23:02:01.834 INFO ProgressMeter - chr3:920014 17.8 11440 641.4
23:02:13.100 INFO ProgressMeter - chr3:12356151 18.0 11550 640.8
23:02:24.560 INFO ProgressMeter - chr3:12363838 18.2 11610 637.4
23:02:35.003 INFO ProgressMeter - chr3:12373301 18.4 11670 634.6
23:02:45.388 INFO ProgressMeter - chr3:12585930 18.6 11740 632.4
23:02:55.826 INFO ProgressMeter - chr3:38140755 18.7 11840 631.9
23:03:06.320 INFO ProgressMeter - chr3:49362494 18.9 11940 631.4
23:03:16.456 INFO ProgressMeter - chr3:52576539 19.1 12060 632.1
23:03:27.116 INFO ProgressMeter - chr3:89395961 19.3 12190 633.0
23:03:37.273 INFO ProgressMeter - chr3:136502607 19.4 12310 633.6
23:03:47.388 INFO ProgressMeter - chr3:142550130 19.6 12440 634.8
23:03:57.441 INFO ProgressMeter - chr3:181712710 19.8 12570 636.0
23:04:07.754 INFO ProgressMeter - chr3:186786521 19.9 12680 636.0
23:04:18.063 INFO ProgressMeter - chr4:1799745 20.1 12820 637.6
23:04:28.816 INFO ProgressMeter - chr4:54262543 20.3 12960 638.8
23:04:39.025 INFO ProgressMeter - chr4:55092615 20.5 13070 638.9
23:04:49.061 INFO ProgressMeter - chr4:83462839 20.6 13190 639.5
23:04:59.107 INFO ProgressMeter - chr4:105242303 20.8 13280 638.7
23:05:09.185 INFO ProgressMeter - chr4:168742391 21.0 13410 639.8
23:05:19.248 INFO ProgressMeter - chr4:186663297 21.1 13510 639.5
23:05:29.453 INFO ProgressMeter - chr5:38954772 21.3 13610 639.0
23:05:39.824 INFO ProgressMeter - chr5:56884662 21.5 13750 640.4
23:05:50.272 INFO ProgressMeter - chr5:112838258 21.6 13910 642.7
23:06:01.011 INFO ProgressMeter - chr5:132609281 21.8 14010 642.0
23:06:11.437 INFO ProgressMeter - chr5:150059698 22.0 14130 642.4
23:06:22.038 INFO ProgressMeter - chr5:171391303 22.2 14250 642.7
23:06:32.461 INFO ProgressMeter - chr5:177209948 22.3 14340 641.7
23:06:42.660 INFO ProgressMeter - chr6:401422 22.5 14470 642.6
23:06:52.712 INFO ProgressMeter - chr6:26250277 22.7 14610 644.0
23:07:02.774 INFO ProgressMeter - chr6:30714025 22.9 14690 642.8
23:07:12.832 INFO ProgressMeter - chr6:41940950 23.0 14820 643.8
23:07:23.059 INFO ProgressMeter - chr6:111700138 23.2 14960 645.1
23:07:34.046 INFO ProgressMeter - chr6:117321887 23.4 15030 643.0
23:07:45.188 INFO ProgressMeter - chr6:117330563 23.6 15110 641.4
23:07:58.356 INFO ProgressMeter - chr6:117338829 23.8 15180 638.4
23:08:08.470 INFO ProgressMeter - chr6:135204827 23.9 15280 638.1
23:08:19.288 INFO ProgressMeter - chr6:135212627 24.1 15340 635.8
23:08:29.482 INFO ProgressMeter - chr6:137881033 24.3 15420 634.6
23:08:40.403 INFO ProgressMeter - chr6:156778692 24.5 15530 634.4
23:08:50.603 INFO ProgressMeter - chr6:163534980 24.6 15660 635.3
23:09:01.147 INFO ProgressMeter - chr7:13906758 24.8 15770 635.2
23:09:12.053 INFO ProgressMeter - chr7:13937087 25.0 15830 633.0
23:09:23.164 INFO ProgressMeter - chr7:13945407 25.2 15900 631.1
23:09:33.589 INFO ProgressMeter - chr7:13952288 25.4 15950 628.8
23:09:45.208 INFO ProgressMeter - chr7:13960491 25.6 16020 626.8
23:09:59.197 INFO ProgressMeter - chr7:13971662 25.8 16100 624.2
23:10:09.499 INFO ProgressMeter - chr7:13977531 26.0 16140 621.6
23:10:22.983 INFO ProgressMeter - chr7:13989693 26.2 16220 619.3
23:10:34.405 INFO ProgressMeter - chr7:55167181 26.4 16320 618.7
23:10:44.599 INFO ProgressMeter - chr7:55178373 26.5 16380 617.0
23:10:54.814 INFO ProgressMeter - chr7:78343776 26.7 16470 616.4
23:11:05.372 INFO ProgressMeter - chr7:102197279 26.9 16610 617.6
23:11:15.748 INFO ProgressMeter - chr7:116771496 27.1 16720 617.7
23:11:26.310 INFO ProgressMeter - chr7:140792453 27.2 16830 617.7
23:11:36.926 INFO ProgressMeter - chr7:152148969 27.4 16970 618.9
23:11:47.037 INFO ProgressMeter - chr7:152220678 27.6 17060 618.3
23:11:57.415 INFO ProgressMeter - chr8:32548728 27.8 17190 619.2
23:12:07.610 INFO ProgressMeter - chr8:37838954 27.9 17290 619.0
23:12:17.983 INFO ProgressMeter - chr8:42048662 28.1 17410 619.4
23:12:28.091 INFO ProgressMeter - chr8:47935826 28.3 17530 620.0
23:12:38.820 INFO ProgressMeter - chr8:89971171 28.5 17670 621.0
23:12:48.833 INFO ProgressMeter - chr8:127740939 28.6 17770 620.9
23:12:59.076 INFO ProgressMeter - chr9:5534926 28.8 17900 621.7
23:13:09.217 INFO ProgressMeter - chr9:35074106 29.0 18020 622.2
23:13:20.790 INFO ProgressMeter - chr9:84742886 29.2 18120 621.6
23:13:31.286 INFO ProgressMeter - chr9:84861038 29.3 18170 619.5
23:13:42.014 INFO ProgressMeter - chr9:84873095 29.5 18230 617.8
23:13:53.461 INFO ProgressMeter - chr9:85024803 29.7 18310 616.6
23:14:03.704 INFO ProgressMeter - chr9:95469007 29.9 18400 616.0
23:14:14.544 INFO ProgressMeter - chr9:130886079 30.0 18530 616.7
23:14:25.238 INFO ProgressMeter - chr9:136511150 30.2 18630 616.3
23:14:35.240 INFO ProgressMeter - chrX:40074668 30.4 18760 617.2
23:14:45.499 INFO ProgressMeter - chrX:49030188 30.6 18890 618.0
23:14:55.866 INFO ProgressMeter - chrX:53196908 30.7 18970 617.2
23:15:07.061 INFO ProgressMeter - chrX:64192574 30.9 19090 617.3
23:15:17.078 INFO ProgressMeter - chrX:71135090 31.1 19210 617.9
23:15:27.126 INFO ProgressMeter - chrX:77652112 31.3 19320 618.1
23:15:39.429 INFO ProgressMeter - chrX:124066173 31.5 19460 618.5
23:15:46.899 INFO Mutect2 - 426330 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
70 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
426402 total reads filtered out of 52297790 reads processed
23:15:46.900 INFO ProgressMeter - chrY:19773323 31.6 19586 620.0
23:15:46.900 INFO ProgressMeter - Traversal complete. Processed 19586 total regions in 31.6 minutes.
23:15:46.915 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 4.092236924
23:15:46.916 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 155.224035433
23:15:46.916 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 6.07 sec
23:15:46.916 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:15:46 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 31.60 minutes.
Runtime.totalMemory()=2239758336
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 LS0921_tumor.bam --tumor-sample LS0921 -L TST500C_manifest.bed -O LS0921.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:15:48.249 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
23:15:48.367 INFO FilterMutectCalls - ------------------------------------------------------------
23:15:48.369 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:15:48.369 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:15:48.369 INFO FilterMutectCalls - Executing as ?@nf-3d2d0aed8b32a32f069823bdaf9bf383-988fd-w28vz on Linux v6.12.88 amd64
23:15:48.369 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:15:48.369 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:15:48 PM GMT
23:15:48.369 INFO FilterMutectCalls - ------------------------------------------------------------
23:15:48.369 INFO FilterMutectCalls - ------------------------------------------------------------
23:15:48.370 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:15:48.370 INFO FilterMutectCalls - Picard Version: 3.1.1
23:15:48.370 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:15:48.370 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:15:48.370 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:15:48.370 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:15:48.370 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:15:48.370 INFO FilterMutectCalls - Deflater: IntelDeflater
23:15:48.371 INFO FilterMutectCalls - Inflater: IntelInflater
23:15:48.371 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:15:48.371 INFO FilterMutectCalls - Requester pays: disabled
23:15:48.371 INFO FilterMutectCalls - Initializing engine
23:15:48.496 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.KmgEqbjZlB/LS0921.mutect2.raw.vcf.gz
23:15:48.604 INFO FilterMutectCalls - Done initializing engine
23:15:48.675 INFO ProgressMeter - Starting traversal
23:15:48.676 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:15:48.678 INFO FilterMutectCalls - Starting pass 0 through the variants
23:15:49.617 INFO FilterMutectCalls - Finished pass 0 through the variants
23:15:49.997 INFO FilterMutectCalls - Starting pass 1 through the variants
23:15:50.865 INFO FilterMutectCalls - Finished pass 1 through the variants
23:15:50.954 INFO FilterMutectCalls - Starting pass 2 through the variants
23:15:51.782 INFO FilterMutectCalls - Finished pass 2 through the variants
23:15:51.784 INFO FilterMutectCalls - Starting pass 3 through the variants
23:15:52.509 INFO FilterMutectCalls - Finished pass 3 through the variants
23:15:52.515 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:15:52.516 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:15:52.516 INFO ProgressMeter - chr4:105236262 0.1 9916 154937.5
23:15:52.516 INFO ProgressMeter - Traversal complete. Processed 9916 total variants in 0.1 minutes.
23:15:52.527 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:15:52 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.07 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 FilterMutectCalls -R hg38.fa -V LS0921.mutect2.raw.vcf.gz --stats LS0921.mutect2.raw.vcf.gz.stats -O LS0921.mutect2.filtered.vcf.gz
23:15:53.925 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
23:15:54.037 INFO SelectVariants - ------------------------------------------------------------
23:15:54.040 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:15:54.040 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:15:54.040 INFO SelectVariants - Executing as ?@nf-3d2d0aed8b32a32f069823bdaf9bf383-988fd-w28vz on Linux v6.12.88 amd64
23:15:54.040 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:15:54.040 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:15:53 PM GMT
23:15:54.040 INFO SelectVariants - ------------------------------------------------------------
23:15:54.040 INFO SelectVariants - ------------------------------------------------------------
23:15:54.041 INFO SelectVariants - HTSJDK Version: 4.1.0
23:15:54.041 INFO SelectVariants - Picard Version: 3.1.1
23:15:54.041 INFO SelectVariants - Built for Spark Version: 3.5.0
23:15:54.041 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:15:54.041 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:15:54.041 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:15:54.041 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:15:54.041 INFO SelectVariants - Deflater: IntelDeflater
23:15:54.041 INFO SelectVariants - Inflater: IntelInflater
23:15:54.041 INFO SelectVariants - GCS max retries/reopens: 20
23:15:54.042 INFO SelectVariants - Requester pays: disabled
23:15:54.042 INFO SelectVariants - Initializing engine
23:15:54.150 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.KmgEqbjZlB/LS0921.mutect2.filtered.vcf.gz
23:15:54.258 INFO SelectVariants - Done initializing engine
23:15:54.296 INFO ProgressMeter - Starting traversal
23:15:54.297 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:15:54.358 INFO ProgressMeter - chr7:6401978 0.0 2479 2521016.9
23:15:54.358 INFO ProgressMeter - Traversal complete. Processed 2479 total variants in 0.0 minutes.
23:15:54.369 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:15:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0921.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0921.mutect2.pass.vcf.gz