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/LS0915/LS0915_tumor.bam.bai
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/e9/4c46c2c67d88e3cad1ee956a953c15/.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/e9/4c46c2c67d88e3cad1ee956a953c15/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0915/LS0915_tumor.bam
==> STAGING COMPLETE (10 inputs)
22:44:27.538 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
22:44:27.640 INFO Mutect2 - ------------------------------------------------------------
22:44:27.643 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:27.643 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:27.643 INFO Mutect2 - Executing as ?@nf-e94c46c2c67d88e3cad1ee956a953c15-ac90c-7nn6d on Linux v6.12.88 amd64
22:44:27.643 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:27.643 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:27 PM GMT
22:44:27.644 INFO Mutect2 - ------------------------------------------------------------
22:44:27.644 INFO Mutect2 - ------------------------------------------------------------
22:44:27.644 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:27.644 INFO Mutect2 - Picard Version: 3.1.1
22:44:27.644 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:27.644 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:27.645 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:27.645 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:27.645 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:27.645 INFO Mutect2 - Deflater: IntelDeflater
22:44:27.645 INFO Mutect2 - Inflater: IntelInflater
22:44:27.645 INFO Mutect2 - GCS max retries/reopens: 20
22:44:27.645 INFO Mutect2 - Requester pays: disabled
22:44:27.646 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.RHsHotmYjW/LS0915_tumor.bam.bai is older than BAM /tmp/nxf.RHsHotmYjW/LS0915_tumor.bam
22:44:27.800 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.RHsHotmYjW/af-only-gnomad.hg38.vcf.gz
22:44:27.926 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.RHsHotmYjW/TST500C_manifest.bed
22:44:27.960 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:27.988 INFO Mutect2 - Done initializing engine
22:44:27.999 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
22:44:28.000 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
22:44:28.001 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:28.001 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:28.011 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
22:44:28.019 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:28.020 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:28.020 INFO IntelPairHmm - Available threads: 384
22:44:28.020 INFO IntelPairHmm - Requested threads: 4
22:44:28.021 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:28.066 INFO ProgressMeter - Starting traversal
22:44:28.066 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:38.787 INFO ProgressMeter - chr1:15911099 0.2 150 839.6
22:44:49.294 INFO ProgressMeter - chr1:23558958 0.4 270 763.1
22:44:59.512 INFO ProgressMeter - chr1:39898101 0.5 390 744.1
22:45:09.847 INFO ProgressMeter - chr1:46261267 0.7 510 732.4
22:45:20.067 INFO ProgressMeter - chr1:117623812 0.9 700 807.7
22:45:31.126 INFO ProgressMeter - chr1:156873259 1.1 820 780.2
22:45:41.542 INFO ProgressMeter - chr1:162776228 1.2 960 783.9
22:45:51.641 INFO ProgressMeter - chr1:206480445 1.4 1170 840.0
22:46:02.346 INFO ProgressMeter - chr10:8073946 1.6 1320 840.1
22:46:12.378 INFO ProgressMeter - chr10:43109029 1.7 1450 834.0
22:46:22.885 INFO ProgressMeter - chr10:68645435 1.9 1570 820.4
22:46:33.447 INFO ProgressMeter - chr10:110584203 2.1 1760 842.2
22:46:43.588 INFO ProgressMeter - chr11:8263336 2.3 1920 850.1
22:46:55.615 INFO ProgressMeter - chr11:69701730 2.5 2100 854.0
22:47:06.297 INFO ProgressMeter - chr11:69810832 2.6 2190 830.4
22:47:16.339 INFO ProgressMeter - chr11:77344163 2.8 2290 816.5
22:47:26.783 INFO ProgressMeter - chr11:101127614 3.0 2410 809.1
22:47:37.123 INFO ProgressMeter - chr11:108251903 3.2 2470 783.9
22:47:47.353 INFO ProgressMeter - chr11:118473652 3.3 2580 776.8
22:47:57.974 INFO ProgressMeter - chr11:118522159 3.5 2670 763.2
22:48:08.412 INFO ProgressMeter - chr11:128458957 3.7 2760 751.5
22:48:19.140 INFO ProgressMeter - chr11:128587486 3.9 2810 729.6
22:48:29.160 INFO ProgressMeter - chr12:927143 4.0 2910 724.2
22:48:39.341 INFO ProgressMeter - chr12:4441124 4.2 3010 718.7
22:48:49.620 INFO ProgressMeter - chr12:11853690 4.4 3100 711.1
22:49:00.740 INFO ProgressMeter - chr12:11860716 4.5 3170 697.5
22:49:11.746 INFO ProgressMeter - chr12:11869815 4.7 3240 685.3
22:49:22.334 INFO ProgressMeter - chr12:49026364 4.9 3410 695.3
22:49:32.725 INFO ProgressMeter - chr12:56085057 5.1 3580 705.1
22:49:43.264 INFO ProgressMeter - chr12:68836901 5.3 3770 717.6
22:49:53.601 INFO ProgressMeter - chr13:20983481 5.4 3970 731.7
22:50:04.240 INFO ProgressMeter - chr13:28368095 5.6 4120 735.3
22:50:14.948 INFO ProgressMeter - chr13:32336849 5.8 4200 726.5
22:50:25.504 INFO ProgressMeter - chr13:72763583 6.0 4330 726.8
22:50:35.755 INFO ProgressMeter - chr14:23182978 6.1 4510 735.9
22:50:45.828 INFO ProgressMeter - chr14:68477803 6.3 4650 738.6
22:50:56.215 INFO ProgressMeter - chr15:34355019 6.5 4820 745.1
22:51:06.300 INFO ProgressMeter - chr15:67181239 6.6 4990 751.8
22:51:16.682 INFO ProgressMeter - chr15:93024370 6.8 5200 763.6
22:51:26.800 INFO ProgressMeter - chr16:3608428 7.0 5410 775.2
22:51:36.838 INFO ProgressMeter - chr16:23629825 7.1 5570 779.4
22:51:47.349 INFO ProgressMeter - chr16:72795931 7.3 5750 785.4
22:51:57.502 INFO ProgressMeter - chr16:89739131 7.5 5910 789.0
22:52:07.588 INFO ProgressMeter - chr17:16032305 7.7 6100 796.5
22:52:17.813 INFO ProgressMeter - chr17:39471503 7.8 6310 806.0
22:52:28.037 INFO ProgressMeter - chr17:43074329 8.0 6560 820.0
22:52:38.543 INFO ProgressMeter - chr17:43541947 8.2 6710 820.8
22:52:49.437 INFO ProgressMeter - chr17:60600413 8.4 6890 824.5
22:53:00.212 INFO ProgressMeter - chr18:22171303 8.5 7090 830.6
22:53:10.265 INFO ProgressMeter - chr19:3094650 8.7 7320 841.1
22:53:20.636 INFO ProgressMeter - chr19:10151748 8.9 7490 843.8
22:53:31.179 INFO ProgressMeter - chr19:15179362 9.1 7660 846.2
22:53:41.769 INFO ProgressMeter - chr19:29819173 9.2 7820 847.4
22:53:51.880 INFO ProgressMeter - chr19:41878988 9.4 8010 852.4
22:54:02.229 INFO ProgressMeter - chr19:45414859 9.6 8140 850.6
22:54:12.697 INFO ProgressMeter - chr2:17768736 9.7 8300 851.8
22:54:22.989 INFO ProgressMeter - chr2:29223818 9.9 8430 850.2
22:54:34.388 INFO ProgressMeter - chr2:47414562 10.1 8570 848.1
22:54:44.839 INFO ProgressMeter - chr2:98576987 10.3 8730 849.3
22:54:55.041 INFO ProgressMeter - chr2:113224040 10.4 8870 848.8
22:55:05.334 INFO ProgressMeter - chr2:127289725 10.6 8990 846.4
22:55:15.382 INFO ProgressMeter - chr2:189844047 10.8 9180 850.9
22:55:25.954 INFO ProgressMeter - chr2:197409848 11.0 9270 845.4
22:55:36.710 INFO ProgressMeter - chr2:222201189 11.1 9400 843.5
22:55:47.235 INFO ProgressMeter - chr2:222214856 11.3 9490 838.4
22:55:57.511 INFO ProgressMeter - chr2:241852919 11.5 9610 836.3
22:56:07.730 INFO ProgressMeter - chr20:41080083 11.7 9750 836.1
22:56:17.766 INFO ProgressMeter - chr20:58854355 11.8 9890 836.1
22:56:30.640 INFO ProgressMeter - chr21:41491048 12.0 10060 835.3
22:56:41.151 INFO ProgressMeter - chr21:41507245 12.2 10150 830.7
22:56:51.519 INFO ProgressMeter - chr22:29283668 12.4 10370 836.9
22:57:01.736 INFO ProgressMeter - chr3:10081344 12.6 10540 839.1
22:57:11.800 INFO ProgressMeter - chr3:12364106 12.7 10640 835.9
22:57:22.427 INFO ProgressMeter - chr3:12379640 12.9 10740 832.2
22:57:32.983 INFO ProgressMeter - chr3:47062277 13.1 10900 833.2
22:57:43.161 INFO ProgressMeter - chr3:52563281 13.3 11060 834.6
22:57:53.291 INFO ProgressMeter - chr3:135167002 13.4 11240 837.5
22:58:03.339 INFO ProgressMeter - chr3:142523991 13.6 11400 839.0
22:58:13.629 INFO ProgressMeter - chr3:185480340 13.8 11570 840.9
22:58:23.676 INFO ProgressMeter - chr3:196077062 13.9 11720 841.5
22:58:34.069 INFO ProgressMeter - chr4:54699628 14.1 11930 846.1
22:58:44.345 INFO ProgressMeter - chr4:98929093 14.3 12100 847.9
22:58:54.844 INFO ProgressMeter - chr4:186596784 14.4 12280 850.0
22:59:04.957 INFO ProgressMeter - chr5:39003556 14.6 12460 852.6
22:59:15.882 INFO ProgressMeter - chr5:112827195 14.8 12680 856.9
22:59:25.976 INFO ProgressMeter - chr5:122451001 15.0 12760 852.6
22:59:36.493 INFO ProgressMeter - chr5:150115795 15.1 12920 853.3
22:59:47.221 INFO ProgressMeter - chr5:177092644 15.3 13060 852.5
22:59:57.289 INFO ProgressMeter - chr5:180612504 15.5 13180 851.0
23:00:12.330 INFO ProgressMeter - chr6:30700463 15.7 13370 849.6
23:00:22.677 INFO ProgressMeter - chr6:36682751 15.9 13520 849.8
23:00:33.020 INFO ProgressMeter - chr6:112064860 16.1 13690 851.2
23:00:43.600 INFO ProgressMeter - chr6:117330150 16.3 13780 847.5
23:00:54.481 INFO ProgressMeter - chr6:135204840 16.4 13910 846.1
23:01:04.859 INFO ProgressMeter - chr6:135217539 16.6 13990 842.1
23:01:15.447 INFO ProgressMeter - chr6:157133188 16.8 14140 842.2
23:01:25.983 INFO ProgressMeter - chr7:6003970 17.0 14310 843.5
23:01:37.143 INFO ProgressMeter - chr7:13932090 17.2 14390 839.0
23:01:48.292 INFO ProgressMeter - chr7:13943032 17.3 14470 834.6
23:01:59.698 INFO ProgressMeter - chr7:13950695 17.5 14530 829.0
23:02:10.196 INFO ProgressMeter - chr7:13961194 17.7 14600 824.8
23:02:21.829 INFO ProgressMeter - chr7:13970842 17.9 14680 820.3
23:02:32.233 INFO ProgressMeter - chr7:13977430 18.1 14730 815.2
23:02:42.702 INFO ProgressMeter - chr7:13983875 18.2 14780 810.1
23:02:52.947 INFO ProgressMeter - chr7:41690192 18.4 14820 804.8
23:03:03.989 INFO ProgressMeter - chr7:55169330 18.6 14910 801.7
23:03:14.685 INFO ProgressMeter - chr7:55180501 18.8 14980 797.8
23:03:24.963 INFO ProgressMeter - chr7:92707456 18.9 15120 798.0
23:03:35.026 INFO ProgressMeter - chr7:116778810 19.1 15280 799.3
23:03:45.232 INFO ProgressMeter - chr7:140920436 19.3 15410 799.0
23:03:55.692 INFO ProgressMeter - chr7:152183067 19.5 15550 799.1
23:04:05.902 INFO ProgressMeter - chr8:32743102 19.6 15710 800.3
23:04:15.999 INFO ProgressMeter - chr8:41949220 19.8 15860 801.1
23:04:26.261 INFO ProgressMeter - chr8:75606427 20.0 16080 805.2
23:04:37.392 INFO ProgressMeter - chr8:127732363 20.2 16160 801.8
23:04:47.788 INFO ProgressMeter - chr8:127739623 20.3 16190 796.4
23:04:58.140 INFO ProgressMeter - chr9:5077451 20.5 16280 794.1
23:05:08.524 INFO ProgressMeter - chr9:83971651 20.7 16460 796.2
23:05:20.408 INFO ProgressMeter - chr9:84815425 20.9 16550 792.9
23:05:30.551 INFO ProgressMeter - chr9:84872654 21.0 16610 789.4
23:05:41.167 INFO ProgressMeter - chr9:85025759 21.2 16690 786.6
23:05:51.654 INFO ProgressMeter - chr9:130854933 21.4 16840 787.2
23:06:01.992 INFO ProgressMeter - chr9:136518179 21.6 16970 786.9
23:06:12.203 INFO ProgressMeter - chrX:49036627 21.7 17210 791.8
23:06:22.412 INFO ProgressMeter - chrX:77681635 21.9 17530 800.2
23:06:27.623 INFO Mutect2 - 334131 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
1 read(s) filtered by: ReadLengthReadFilter
77 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
334209 total reads filtered out of 40932166 reads processed
23:06:27.623 INFO ProgressMeter - chrY:19742782 22.0 17737 806.5
23:06:27.623 INFO ProgressMeter - Traversal complete. Processed 17737 total regions in 22.0 minutes.
23:06:27.637 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 3.0082645660000003
23:06:27.637 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 112.197420116
23:06:27.637 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 4.80 sec
23:06:27.638 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:06:27 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 22.00 minutes.
Runtime.totalMemory()=3154116608
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 LS0915_tumor.bam --tumor-sample LS0915 -L TST500C_manifest.bed -O LS0915.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:06:29.008 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
23:06:29.117 INFO FilterMutectCalls - ------------------------------------------------------------
23:06:29.120 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:06:29.120 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:06:29.120 INFO FilterMutectCalls - Executing as ?@nf-e94c46c2c67d88e3cad1ee956a953c15-ac90c-7nn6d on Linux v6.12.88 amd64
23:06:29.120 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:06:29.121 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:06:28 PM GMT
23:06:29.121 INFO FilterMutectCalls - ------------------------------------------------------------
23:06:29.121 INFO FilterMutectCalls - ------------------------------------------------------------
23:06:29.121 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:06:29.122 INFO FilterMutectCalls - Picard Version: 3.1.1
23:06:29.122 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:06:29.122 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:06:29.123 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:06:29.123 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:06:29.123 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:06:29.123 INFO FilterMutectCalls - Deflater: IntelDeflater
23:06:29.123 INFO FilterMutectCalls - Inflater: IntelInflater
23:06:29.123 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:06:29.123 INFO FilterMutectCalls - Requester pays: disabled
23:06:29.123 INFO FilterMutectCalls - Initializing engine
23:06:29.312 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.RHsHotmYjW/LS0915.mutect2.raw.vcf.gz
23:06:29.422 INFO FilterMutectCalls - Done initializing engine
23:06:29.481 INFO ProgressMeter - Starting traversal
23:06:29.481 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:06:29.482 INFO FilterMutectCalls - Starting pass 0 through the variants
23:06:30.180 INFO FilterMutectCalls - Finished pass 0 through the variants
23:06:31.629 INFO FilterMutectCalls - Starting pass 1 through the variants
23:06:32.209 INFO FilterMutectCalls - Finished pass 1 through the variants
23:06:32.560 INFO FilterMutectCalls - Starting pass 2 through the variants
23:06:33.125 INFO FilterMutectCalls - Finished pass 2 through the variants
23:06:33.126 INFO FilterMutectCalls - Starting pass 3 through the variants
23:06:33.721 INFO FilterMutectCalls - Finished pass 3 through the variants
23:06:33.731 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:06:33.732 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:06:33.732 INFO ProgressMeter - chr7:13941638 0.1 9472 133690.9
23:06:33.732 INFO ProgressMeter - Traversal complete. Processed 9472 total variants in 0.1 minutes.
23:06:33.746 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:06:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.08 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 FilterMutectCalls -R hg38.fa -V LS0915.mutect2.raw.vcf.gz --stats LS0915.mutect2.raw.vcf.gz.stats -O LS0915.mutect2.filtered.vcf.gz
23:06:35.134 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
23:06:35.257 INFO SelectVariants - ------------------------------------------------------------
23:06:35.260 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:06:35.260 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:06:35.260 INFO SelectVariants - Executing as ?@nf-e94c46c2c67d88e3cad1ee956a953c15-ac90c-7nn6d on Linux v6.12.88 amd64
23:06:35.260 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:06:35.260 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:06:35 PM GMT
23:06:35.260 INFO SelectVariants - ------------------------------------------------------------
23:06:35.260 INFO SelectVariants - ------------------------------------------------------------
23:06:35.261 INFO SelectVariants - HTSJDK Version: 4.1.0
23:06:35.261 INFO SelectVariants - Picard Version: 3.1.1
23:06:35.261 INFO SelectVariants - Built for Spark Version: 3.5.0
23:06:35.261 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:06:35.261 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:06:35.262 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:06:35.262 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:06:35.262 INFO SelectVariants - Deflater: IntelDeflater
23:06:35.262 INFO SelectVariants - Inflater: IntelInflater
23:06:35.262 INFO SelectVariants - GCS max retries/reopens: 20
23:06:35.262 INFO SelectVariants - Requester pays: disabled
23:06:35.262 INFO SelectVariants - Initializing engine
23:06:35.426 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.RHsHotmYjW/LS0915.mutect2.filtered.vcf.gz
23:06:35.542 INFO SelectVariants - Done initializing engine
23:06:35.580 INFO ProgressMeter - Starting traversal
23:06:35.580 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:06:35.658 INFO ProgressMeter - chr7:13981532 0.0 2368 1894400.0
23:06:35.658 INFO ProgressMeter - Traversal complete. Processed 2368 total variants in 0.0 minutes.
23:06:35.672 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:06:35 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 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 SelectVariants -R hg38.fa -V LS0915.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0915.mutect2.pass.vcf.gz