Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/f2/32d3fe588738f81bf5c5676ed7327a/.command.sh
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0887/LS0887_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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0887/LS0887_tumor.bam
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/f2/32d3fe588738f81bf5c5676ed7327a/.command.run
==> STAGING COMPLETE (10 inputs)
22:44:13.596 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
22:44:13.708 INFO Mutect2 - ------------------------------------------------------------
22:44:13.710 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:13.710 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:13.710 INFO Mutect2 - Executing as ?@nf-f232d3fe588738f81bf5c5676ed7327a-fbd0e-fqmn7 on Linux v6.12.88 amd64
22:44:13.711 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:13.711 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:13 PM GMT
22:44:13.711 INFO Mutect2 - ------------------------------------------------------------
22:44:13.711 INFO Mutect2 - ------------------------------------------------------------
22:44:13.712 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:13.712 INFO Mutect2 - Picard Version: 3.1.1
22:44:13.712 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:13.712 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:13.713 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:13.713 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:13.713 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:13.713 INFO Mutect2 - Deflater: IntelDeflater
22:44:13.713 INFO Mutect2 - Inflater: IntelInflater
22:44:13.713 INFO Mutect2 - GCS max retries/reopens: 20
22:44:13.713 INFO Mutect2 - Requester pays: disabled
22:44:13.714 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.3c3jJTUbbC/LS0887_tumor.bam.bai is older than BAM /tmp/nxf.3c3jJTUbbC/LS0887_tumor.bam
22:44:13.921 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.3c3jJTUbbC/af-only-gnomad.hg38.vcf.gz
22:44:14.040 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.3c3jJTUbbC/TST500C_manifest.bed
22:44:14.079 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:14.109 INFO Mutect2 - Done initializing engine
22:44:14.120 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
22:44:14.121 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
22:44:14.122 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:14.122 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:14.132 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
22:44:14.141 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:14.141 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:14.142 INFO IntelPairHmm - Available threads: 384
22:44:14.142 INFO IntelPairHmm - Requested threads: 4
22:44:14.142 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:14.186 INFO ProgressMeter - Starting traversal
22:44:14.186 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:24.383 INFO ProgressMeter - chr1:11234141 0.2 110 647.4
22:44:34.678 INFO ProgressMeter - chr1:18744911 0.3 220 644.2
22:44:44.902 INFO ProgressMeter - chr1:39895521 0.5 340 664.2
22:44:55.002 INFO ProgressMeter - chr1:64841328 0.7 490 720.3
22:45:05.285 INFO ProgressMeter - chr1:119920227 0.9 630 739.8
22:45:16.654 INFO ProgressMeter - chr1:156881455 1.0 720 691.6
22:45:27.037 INFO ProgressMeter - chr1:179118585 1.2 860 708.3
22:45:37.274 INFO ProgressMeter - chr1:206771354 1.4 1020 736.6
22:45:47.642 INFO ProgressMeter - chr10:8055654 1.6 1130 725.5
22:45:58.356 INFO ProgressMeter - chr10:43114171 1.7 1270 731.5
22:46:08.579 INFO ProgressMeter - chr10:87866449 1.9 1380 723.8
22:46:19.181 INFO ProgressMeter - chr10:112950755 2.1 1530 734.4
22:46:29.374 INFO ProgressMeter - chr10:121562590 2.3 1630 723.4
22:46:39.378 INFO ProgressMeter - chr11:69651409 2.4 1780 735.6
22:46:49.756 INFO ProgressMeter - chr11:69770782 2.6 1850 713.5
22:47:00.568 INFO ProgressMeter - chr11:69812082 2.8 1900 685.2
22:47:10.590 INFO ProgressMeter - chr11:77360148 2.9 1980 673.5
22:47:22.112 INFO ProgressMeter - chr11:102325108 3.1 2090 667.3
22:47:32.889 INFO ProgressMeter - chr11:118505475 3.3 2250 679.4
22:47:43.012 INFO ProgressMeter - chr11:128460663 3.5 2350 675.2
22:47:53.433 INFO ProgressMeter - chr12:4376698 3.7 2490 681.4
22:48:03.585 INFO ProgressMeter - chr12:11854997 3.8 2620 685.3
22:48:13.612 INFO ProgressMeter - chr12:11864314 4.0 2690 674.1
22:48:24.256 INFO ProgressMeter - chr12:45811416 4.2 2830 679.0
22:48:34.899 INFO ProgressMeter - chr12:49041915 4.3 2930 674.3
22:48:44.971 INFO ProgressMeter - chr12:56101527 4.5 3070 680.2
22:48:56.241 INFO ProgressMeter - chr12:68839330 4.7 3220 685.0
22:49:06.325 INFO ProgressMeter - chr12:132675733 4.9 3370 692.1
22:49:17.677 INFO ProgressMeter - chr13:28384883 5.1 3520 695.9
22:49:27.942 INFO ProgressMeter - chr13:32338982 5.2 3600 688.4
22:49:38.106 INFO ProgressMeter - chr13:102862328 5.4 3760 696.5
22:49:48.899 INFO ProgressMeter - chr14:37591663 5.6 3900 699.1
22:49:59.307 INFO ProgressMeter - chr14:104770743 5.8 4050 704.1
22:50:09.373 INFO ProgressMeter - chr15:41736479 5.9 4160 702.7
22:50:20.122 INFO ProgressMeter - chr15:87981224 6.1 4300 705.0
22:50:30.200 INFO ProgressMeter - chr15:98707856 6.3 4460 711.7
22:50:40.836 INFO ProgressMeter - chr16:3729003 6.4 4640 720.0
22:50:51.363 INFO ProgressMeter - chr16:31132007 6.6 4770 720.6
22:51:01.767 INFO ProgressMeter - chr16:72794784 6.8 4890 719.9
22:51:12.746 INFO ProgressMeter - chr16:89281593 7.0 5000 716.7
22:51:23.542 INFO ProgressMeter - chr17:7676665 7.2 5140 718.3
22:51:33.697 INFO ProgressMeter - chr17:31248982 7.3 5320 726.3
22:51:44.317 INFO ProgressMeter - chr17:39727822 7.5 5480 730.5
22:51:54.518 INFO ProgressMeter - chr17:43092882 7.7 5650 736.4
22:52:06.077 INFO ProgressMeter - chr17:43543229 7.9 5760 732.4
22:52:17.048 INFO ProgressMeter - chr17:59947335 8.0 5910 734.4
22:52:27.142 INFO ProgressMeter - chr17:80922722 8.2 6050 736.4
22:52:37.443 INFO ProgressMeter - chr18:58744336 8.4 6200 739.2
22:52:47.849 INFO ProgressMeter - chr19:7141727 8.6 6400 747.6
22:52:58.403 INFO ProgressMeter - chr19:15174066 8.7 6570 752.0
22:53:10.341 INFO ProgressMeter - chr19:29819201 8.9 6730 753.1
22:53:20.566 INFO ProgressMeter - chr19:41248512 9.1 6890 756.6
22:53:30.691 INFO ProgressMeter - chr19:45414925 9.3 7020 756.9
22:53:40.867 INFO ProgressMeter - chr2:17761394 9.4 7150 757.0
22:53:52.019 INFO ProgressMeter - chr2:29224205 9.6 7270 754.9
22:54:02.845 INFO ProgressMeter - chr2:42332394 9.8 7370 751.2
22:54:14.460 INFO ProgressMeter - chr2:96262363 10.0 7500 749.7
22:54:25.459 INFO ProgressMeter - chr2:113221763 10.2 7640 749.9
22:54:36.564 INFO ProgressMeter - chr2:113235258 10.4 7710 743.3
22:54:47.088 INFO ProgressMeter - chr2:141019920 10.5 7870 746.1
22:54:57.122 INFO ProgressMeter - chr2:203871480 10.7 8030 749.4
22:55:08.097 INFO ProgressMeter - chr2:222208396 10.9 8150 747.8
22:55:18.487 INFO ProgressMeter - chr2:224535526 11.1 8240 744.2
22:55:29.069 INFO ProgressMeter - chr20:32800151 11.2 8370 744.1
22:55:39.166 INFO ProgressMeter - chr20:56370483 11.4 8510 745.4
22:55:49.745 INFO ProgressMeter - chr21:41473323 11.6 8640 745.3
22:56:01.351 INFO ProgressMeter - chr21:41493817 11.8 8680 736.5
22:56:11.403 INFO ProgressMeter - chr22:20989623 12.0 8780 734.5
22:56:21.419 INFO ProgressMeter - chr22:28741353 12.1 8920 735.9
22:56:31.961 INFO ProgressMeter - chr22:41158410 12.3 9040 735.2
22:56:43.546 INFO ProgressMeter - chr3:12355184 12.5 9160 733.4
22:56:54.560 INFO ProgressMeter - chr3:12363608 12.7 9210 726.7
22:57:05.014 INFO ProgressMeter - chr3:12376759 12.8 9280 722.3
22:57:15.098 INFO ProgressMeter - chr3:41233527 13.0 9410 723.0
22:57:25.203 INFO ProgressMeter - chr3:52409552 13.2 9550 724.4
22:57:35.359 INFO ProgressMeter - chr3:135162016 13.4 9710 727.2
22:57:45.429 INFO ProgressMeter - chr3:142556381 13.5 9870 730.0
22:57:56.941 INFO ProgressMeter - chr3:186047844 13.7 10020 730.7
22:58:07.090 INFO ProgressMeter - chr4:1807127 13.9 10170 732.6
22:58:17.416 INFO ProgressMeter - chr4:54727216 14.1 10320 734.3
22:58:27.551 INFO ProgressMeter - chr4:80284013 14.2 10430 733.3
22:58:37.681 INFO ProgressMeter - chr4:122894525 14.4 10560 733.8
22:58:47.782 INFO ProgressMeter - chr4:186633682 14.6 10690 734.2
22:58:58.275 INFO ProgressMeter - chr5:44362662 14.7 10840 735.7
22:59:09.403 INFO ProgressMeter - chr5:112839860 14.9 11020 738.6
22:59:19.522 INFO ProgressMeter - chr5:142638303 15.1 11140 738.3
22:59:29.991 INFO ProgressMeter - chr5:156235227 15.3 11270 738.4
22:59:41.137 INFO ProgressMeter - chr5:177210202 15.4 11360 735.3
22:59:51.215 INFO ProgressMeter - chr6:20447100 15.6 11510 737.0
23:00:01.993 INFO ProgressMeter - chr6:30705125 15.8 11630 736.2
23:00:12.210 INFO ProgressMeter - chr6:36684095 16.0 11760 736.5
23:00:22.233 INFO ProgressMeter - chr6:117310117 16.1 11930 739.4
23:00:32.274 INFO ProgressMeter - chr6:117336330 16.3 12020 737.4
23:00:43.003 INFO ProgressMeter - chr6:135207792 16.5 12130 736.0
23:00:54.285 INFO ProgressMeter - chr6:135217952 16.7 12200 731.9
23:01:04.643 INFO ProgressMeter - chr6:157084667 16.8 12320 731.6
23:01:14.680 INFO ProgressMeter - chr7:5991971 17.0 12470 733.2
23:01:25.392 INFO ProgressMeter - chr7:13935115 17.2 12550 730.2
23:01:37.889 INFO ProgressMeter - chr7:13947811 17.4 12630 726.1
23:01:48.517 INFO ProgressMeter - chr7:13957018 17.6 12690 722.2
23:01:59.507 INFO ProgressMeter - chr7:13964575 17.8 12750 718.1
23:02:10.171 INFO ProgressMeter - chr7:13973942 17.9 12810 714.3
23:02:20.863 INFO ProgressMeter - chr7:13982955 18.1 12870 710.6
23:02:31.706 INFO ProgressMeter - chr7:50327636 18.3 12930 706.9
23:02:42.272 INFO ProgressMeter - chr7:55170620 18.5 13010 704.5
23:02:52.521 INFO ProgressMeter - chr7:78019603 18.6 13090 702.3
23:03:02.567 INFO ProgressMeter - chr7:102274288 18.8 13250 704.5
23:03:12.633 INFO ProgressMeter - chr7:140789891 19.0 13380 705.2
23:03:23.343 INFO ProgressMeter - chr7:152177563 19.2 13540 707.0
23:03:35.098 INFO ProgressMeter - chr8:32634041 19.3 13690 707.5
23:03:45.229 INFO ProgressMeter - chr8:41933556 19.5 13810 707.6
23:03:55.640 INFO ProgressMeter - chr8:68044526 19.7 13970 709.5
23:04:05.699 INFO ProgressMeter - chr8:127739551 19.9 14110 710.5
23:04:16.219 INFO ProgressMeter - chr9:8527343 20.0 14280 712.8
23:04:27.144 INFO ProgressMeter - chr9:84743787 20.2 14410 712.8
23:04:38.480 INFO ProgressMeter - chr9:84864902 20.4 14470 709.1
23:04:49.710 INFO ProgressMeter - chr9:85026970 20.6 14550 706.6
23:04:59.977 INFO ProgressMeter - chr9:130887106 20.8 14700 708.0
23:05:09.988 INFO ProgressMeter - chrX:47176498 20.9 14920 712.9
23:05:20.130 INFO ProgressMeter - chrX:71367497 21.1 15210 720.9
23:05:26.583 INFO Mutect2 - 370687 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
78 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
370765 total reads filtered out of 45707214 reads processed
23:05:26.584 INFO ProgressMeter - chrY:20557826 21.2 15473 729.6
23:05:26.584 INFO ProgressMeter - Traversal complete. Processed 15473 total regions in 21.2 minutes.
23:05:26.600 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.9252493800000003
23:05:26.600 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 119.21798234900001
23:05:26.600 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 4.85 sec
23:05:26.601 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:05:26 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 21.22 minutes.
Runtime.totalMemory()=3137339392
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 LS0887_tumor.bam --tumor-sample LS0887 -L TST500C_manifest.bed -O LS0887.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:05:27.964 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
23:05:28.099 INFO FilterMutectCalls - ------------------------------------------------------------
23:05:28.101 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:05:28.102 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:05:28.102 INFO FilterMutectCalls - Executing as ?@nf-f232d3fe588738f81bf5c5676ed7327a-fbd0e-fqmn7 on Linux v6.12.88 amd64
23:05:28.102 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:05:28.102 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:05:27 PM GMT
23:05:28.102 INFO FilterMutectCalls - ------------------------------------------------------------
23:05:28.102 INFO FilterMutectCalls - ------------------------------------------------------------
23:05:28.103 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:05:28.104 INFO FilterMutectCalls - Picard Version: 3.1.1
23:05:28.104 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:05:28.104 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:05:28.104 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:05:28.104 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:05:28.104 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:05:28.105 INFO FilterMutectCalls - Deflater: IntelDeflater
23:05:28.105 INFO FilterMutectCalls - Inflater: IntelInflater
23:05:28.105 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:05:28.105 INFO FilterMutectCalls - Requester pays: disabled
23:05:28.105 INFO FilterMutectCalls - Initializing engine
23:05:28.284 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.3c3jJTUbbC/LS0887.mutect2.raw.vcf.gz
23:05:28.400 INFO FilterMutectCalls - Done initializing engine
23:05:28.461 INFO ProgressMeter - Starting traversal
23:05:28.461 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:05:28.462 INFO FilterMutectCalls - Starting pass 0 through the variants
23:05:29.227 INFO FilterMutectCalls - Finished pass 0 through the variants
23:05:29.612 INFO FilterMutectCalls - Starting pass 1 through the variants
23:05:30.230 INFO FilterMutectCalls - Finished pass 1 through the variants
23:05:30.315 INFO FilterMutectCalls - Starting pass 2 through the variants
23:05:30.922 INFO FilterMutectCalls - Finished pass 2 through the variants
23:05:30.924 INFO FilterMutectCalls - Starting pass 3 through the variants
23:05:31.499 INFO FilterMutectCalls - Finished pass 3 through the variants
23:05:31.509 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:05:31.510 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:05:31.510 INFO ProgressMeter - chr6:29943377 0.1 8672 170708.7
23:05:31.510 INFO ProgressMeter - Traversal complete. Processed 8672 total variants in 0.1 minutes.
23:05:31.521 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:05:31 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=645922816
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 LS0887.mutect2.raw.vcf.gz --stats LS0887.mutect2.raw.vcf.gz.stats -O LS0887.mutect2.filtered.vcf.gz
23:05:32.932 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
23:05:33.058 INFO SelectVariants - ------------------------------------------------------------
23:05:33.061 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:05:33.061 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:05:33.061 INFO SelectVariants - Executing as ?@nf-f232d3fe588738f81bf5c5676ed7327a-fbd0e-fqmn7 on Linux v6.12.88 amd64
23:05:33.061 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:05:33.062 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:05:32 PM GMT
23:05:33.062 INFO SelectVariants - ------------------------------------------------------------
23:05:33.062 INFO SelectVariants - ------------------------------------------------------------
23:05:33.063 INFO SelectVariants - HTSJDK Version: 4.1.0
23:05:33.063 INFO SelectVariants - Picard Version: 3.1.1
23:05:33.063 INFO SelectVariants - Built for Spark Version: 3.5.0
23:05:33.063 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:05:33.063 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:05:33.063 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:05:33.063 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:05:33.063 INFO SelectVariants - Deflater: IntelDeflater
23:05:33.063 INFO SelectVariants - Inflater: IntelInflater
23:05:33.063 INFO SelectVariants - GCS max retries/reopens: 20
23:05:33.063 INFO SelectVariants - Requester pays: disabled
23:05:33.064 INFO SelectVariants - Initializing engine
23:05:33.231 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.3c3jJTUbbC/LS0887.mutect2.filtered.vcf.gz
23:05:33.350 INFO SelectVariants - Done initializing engine
23:05:33.390 INFO ProgressMeter - Starting traversal
23:05:33.390 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:05:33.455 INFO ProgressMeter - chr8:32634099 0.0 2168 2064761.9
23:05:33.455 INFO ProgressMeter - Traversal complete. Processed 2168 total variants in 0.0 minutes.
23:05:33.466 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:05:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=318767104
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 LS0887.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0887.mutect2.pass.vcf.gz