22:44:27.782 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
22:44:27.887 INFO Mutect2 - ------------------------------------------------------------
22:44:27.889 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:27.890 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:27.890 INFO Mutect2 - Executing as ?@nf-55d075341560335644e93ff81c966a30-bae08-zx9sb on Linux v6.12.88 amd64
22:44:27.890 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:27.890 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:27 PM GMT
22:44:27.890 INFO Mutect2 - ------------------------------------------------------------
22:44:27.890 INFO Mutect2 - ------------------------------------------------------------
22:44:27.891 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:27.891 INFO Mutect2 - Picard Version: 3.1.1
22:44:27.891 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:27.891 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:27.891 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:27.892 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:27.892 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:27.892 INFO Mutect2 - Deflater: IntelDeflater
22:44:27.892 INFO Mutect2 - Inflater: IntelInflater
22:44:27.892 INFO Mutect2 - GCS max retries/reopens: 20
22:44:27.892 INFO Mutect2 - Requester pays: disabled
22:44:27.892 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.xa9ZVmeUpZ/LS0886_tumor.bam.bai is older than BAM /tmp/nxf.xa9ZVmeUpZ/LS0886_tumor.bam
22:44:28.067 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.xa9ZVmeUpZ/af-only-gnomad.hg38.vcf.gz
22:44:28.184 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.xa9ZVmeUpZ/TST500C_manifest.bed
22:44:28.220 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:28.251 INFO Mutect2 - Done initializing engine
22:44:28.262 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
22:44:28.264 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
22:44:28.265 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:28.265 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:28.275 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
22:44:28.283 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:28.284 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:28.284 INFO IntelPairHmm - Available threads: 384
22:44:28.284 INFO IntelPairHmm - Requested threads: 4
22:44:28.284 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:28.325 INFO ProgressMeter - Starting traversal
22:44:28.325 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:38.590 INFO ProgressMeter - chr1:15922247 0.2 140 818.6
22:44:48.599 INFO ProgressMeter - chr1:26731600 0.3 270 799.1
22:44:58.759 INFO ProgressMeter - chr1:46278070 0.5 470 926.6
22:45:08.996 INFO ProgressMeter - chr1:119935338 0.7 670 988.4
22:45:19.247 INFO ProgressMeter - chr1:162755662 0.8 840 989.8
22:45:29.324 INFO ProgressMeter - chr1:226383177 1.0 1070 1052.5
22:45:39.464 INFO ProgressMeter - chr10:43077257 1.2 1250 1054.3
22:45:50.199 INFO ProgressMeter - chr10:68646436 1.4 1380 1011.3
22:46:01.182 INFO ProgressMeter - chr10:121480878 1.5 1600 1033.9
22:46:11.483 INFO ProgressMeter - chr11:67433993 1.7 1770 1029.5
22:46:21.868 INFO ProgressMeter - chr11:69779169 1.9 1920 1014.6
22:46:32.413 INFO ProgressMeter - chr11:77374496 2.1 2030 981.6
22:46:42.437 INFO ProgressMeter - chr11:102335964 2.2 2150 961.9
22:46:52.493 INFO ProgressMeter - chr11:118521895 2.4 2320 965.5
22:47:03.458 INFO ProgressMeter - chr11:128812674 2.6 2460 951.4
22:47:13.632 INFO ProgressMeter - chr12:6599771 2.8 2660 965.5
22:47:23.867 INFO ProgressMeter - chr12:11865598 2.9 2760 943.4
22:47:34.394 INFO ProgressMeter - chr12:49031732 3.1 2950 951.3
22:47:44.641 INFO ProgressMeter - chr12:56099836 3.3 3130 956.6
22:47:54.779 INFO ProgressMeter - chr12:105934409 3.4 3310 962.0
22:48:05.021 INFO ProgressMeter - chr13:21695777 3.6 3510 971.9
22:48:15.819 INFO ProgressMeter - chr13:32337791 3.8 3670 967.9
22:48:26.059 INFO ProgressMeter - chr13:109756302 4.0 3870 976.7
22:48:36.358 INFO ProgressMeter - chr14:95091201 4.1 4110 994.2
22:48:47.239 INFO ProgressMeter - chr15:41749477 4.3 4290 994.2
22:48:57.791 INFO ProgressMeter - chr15:90760592 4.5 4510 1004.2
22:49:07.816 INFO ProgressMeter - chr16:3589101 4.7 4740 1017.6
22:49:18.325 INFO ProgressMeter - chr16:50777823 4.8 4930 1020.0
22:49:28.752 INFO ProgressMeter - chr16:81880908 5.0 5090 1016.6
22:49:39.208 INFO ProgressMeter - chr17:7677737 5.2 5280 1019.0
22:49:49.397 INFO ProgressMeter - chr17:39524672 5.4 5540 1035.3
22:49:59.867 INFO ProgressMeter - chr17:43063872 5.5 5750 1040.6
22:50:10.884 INFO ProgressMeter - chr17:43539847 5.7 5890 1031.7
22:50:21.259 INFO ProgressMeter - chr17:60600413 5.9 6050 1028.5
22:50:31.284 INFO ProgressMeter - chr18:44876544 6.0 6270 1036.5
22:50:41.516 INFO ProgressMeter - chr19:7150495 6.2 6550 1053.1
22:50:52.180 INFO ProgressMeter - chr19:17843775 6.4 6820 1066.0
22:51:02.615 INFO ProgressMeter - chr19:41237942 6.6 7040 1071.3
22:51:13.717 INFO ProgressMeter - chr19:45419096 6.8 7200 1065.6
22:51:24.510 INFO ProgressMeter - chr2:25743227 6.9 7380 1064.0
22:51:35.425 INFO ProgressMeter - chr2:42261119 7.1 7510 1055.0
22:51:47.439 INFO ProgressMeter - chr2:96253806 7.3 7670 1048.0
22:51:58.428 INFO ProgressMeter - chr2:113225912 7.5 7830 1043.8
22:52:08.473 INFO ProgressMeter - chr2:140358015 7.7 7950 1036.6
22:52:19.047 INFO ProgressMeter - chr2:201272896 7.8 8160 1040.1
22:52:30.025 INFO ProgressMeter - chr2:222209792 8.0 8310 1035.1
22:52:40.814 INFO ProgressMeter - chr2:226796728 8.2 8420 1025.8
22:52:51.015 INFO ProgressMeter - chr20:40858508 8.4 8550 1020.5
22:53:01.871 INFO ProgressMeter - chr20:56370483 8.6 8670 1013.0
22:53:12.229 INFO ProgressMeter - chr21:41489656 8.7 8820 1010.1
22:53:22.628 INFO ProgressMeter - chr21:43093100 8.9 8920 1001.7
22:53:32.663 INFO ProgressMeter - chr22:28704198 9.1 9070 999.7
22:53:42.762 INFO ProgressMeter - chr22:29639088 9.2 9180 993.4
22:53:52.763 INFO ProgressMeter - chr3:12354150 9.4 9350 993.9
22:54:02.866 INFO ProgressMeter - chr3:12370796 9.6 9450 986.9
22:54:13.137 INFO ProgressMeter - chr3:47057119 9.7 9640 989.0
22:54:23.390 INFO ProgressMeter - chr3:135259010 9.9 9940 1002.2
22:54:33.410 INFO ProgressMeter - chr3:182945092 10.1 10180 1009.4
22:54:43.971 INFO ProgressMeter - chr4:1806827 10.3 10390 1012.6
22:54:54.680 INFO ProgressMeter - chr4:54736496 10.4 10560 1011.6
22:55:05.026 INFO ProgressMeter - chr4:105242399 10.6 10740 1012.1
22:55:15.316 INFO ProgressMeter - chr5:228183 10.8 10960 1016.4
22:55:25.696 INFO ProgressMeter - chr5:56885930 11.0 11130 1015.9
22:55:36.058 INFO ProgressMeter - chr5:142654528 11.1 11400 1024.4
22:55:46.254 INFO ProgressMeter - chr5:177095106 11.3 11610 1027.5
22:55:56.686 INFO ProgressMeter - chr6:20488379 11.5 11830 1031.1
22:56:07.242 INFO ProgressMeter - chr6:32217993 11.6 11970 1027.6
22:56:17.504 INFO ProgressMeter - chr6:111719803 11.8 12180 1030.5
22:56:27.766 INFO ProgressMeter - chr6:117336861 12.0 12320 1027.5
22:56:38.483 INFO ProgressMeter - chr6:135208901 12.2 12450 1023.1
22:56:48.626 INFO ProgressMeter - chr6:149683518 12.3 12550 1017.2
22:56:58.777 INFO ProgressMeter - chr6:161098305 12.5 12710 1016.2
22:57:09.096 INFO ProgressMeter - chr7:13936374 12.7 12890 1016.6
22:57:19.468 INFO ProgressMeter - chr7:13953173 12.9 13000 1011.5
22:57:31.012 INFO ProgressMeter - chr7:13971158 13.0 13110 1005.0
22:57:41.224 INFO ProgressMeter - chr7:13984220 13.2 13200 998.9
22:57:52.148 INFO ProgressMeter - chr7:55168539 13.4 13310 993.5
22:58:02.396 INFO ProgressMeter - chr7:92623034 13.6 13470 992.8
22:58:12.807 INFO ProgressMeter - chr7:140749285 13.7 13670 994.8
22:58:23.373 INFO ProgressMeter - chr7:152185610 13.9 13880 997.3
22:58:33.442 INFO ProgressMeter - chr8:32742673 14.1 14030 996.1
22:58:43.799 INFO ProgressMeter - chr8:47828166 14.3 14210 996.6
22:58:54.530 INFO ProgressMeter - chr8:127735568 14.4 14430 999.5
22:59:04.709 INFO ProgressMeter - chr9:35077262 14.6 14680 1005.0
22:59:15.953 INFO ProgressMeter - chr9:84866551 14.8 14820 1001.8
22:59:25.972 INFO ProgressMeter - chr9:124119207 15.0 15000 1002.6
22:59:36.140 INFO ProgressMeter - chrX:47571321 15.1 15310 1011.9
22:59:46.260 INFO ProgressMeter - chrX:111147735 15.3 15690 1025.6
22:59:49.667 INFO Mutect2 - 339077 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
45 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
339122 total reads filtered out of 35217923 reads processed
22:59:49.667 INFO ProgressMeter - chrY:19742782 15.4 15848 1032.1
22:59:49.667 INFO ProgressMeter - Traversal complete. Processed 15848 total regions in 15.4 minutes.
22:59:49.683 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.206329965
22:59:49.683 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 82.182939265
22:59:49.683 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 3.63 sec
22:59:49.684 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 10:59:49 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 15.37 minutes.
Runtime.totalMemory()=1140850688
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 LS0886_tumor.bam --tumor-sample LS0886 -L TST500C_manifest.bed -O LS0886.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
22:59:51.021 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
22:59:51.128 INFO FilterMutectCalls - ------------------------------------------------------------
22:59:51.131 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:59:51.131 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
22:59:51.131 INFO FilterMutectCalls - Executing as ?@nf-55d075341560335644e93ff81c966a30-bae08-zx9sb on Linux v6.12.88 amd64
22:59:51.131 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:59:51.132 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 10:59:50 PM GMT
22:59:51.132 INFO FilterMutectCalls - ------------------------------------------------------------
22:59:51.132 INFO FilterMutectCalls - ------------------------------------------------------------
22:59:51.132 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
22:59:51.132 INFO FilterMutectCalls - Picard Version: 3.1.1
22:59:51.133 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
22:59:51.133 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:59:51.133 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:59:51.133 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:59:51.133 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:59:51.133 INFO FilterMutectCalls - Deflater: IntelDeflater
22:59:51.133 INFO FilterMutectCalls - Inflater: IntelInflater
22:59:51.133 INFO FilterMutectCalls - GCS max retries/reopens: 20
22:59:51.133 INFO FilterMutectCalls - Requester pays: disabled
22:59:51.134 INFO FilterMutectCalls - Initializing engine
22:59:51.287 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.xa9ZVmeUpZ/LS0886.mutect2.raw.vcf.gz
22:59:51.396 INFO FilterMutectCalls - Done initializing engine
22:59:51.456 INFO ProgressMeter - Starting traversal
22:59:51.457 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
22:59:51.458 INFO FilterMutectCalls - Starting pass 0 through the variants
22:59:52.103 INFO FilterMutectCalls - Finished pass 0 through the variants
22:59:52.688 INFO FilterMutectCalls - Starting pass 1 through the variants
22:59:53.152 INFO FilterMutectCalls - Finished pass 1 through the variants
22:59:53.323 INFO FilterMutectCalls - Starting pass 2 through the variants
22:59:53.783 INFO FilterMutectCalls - Finished pass 2 through the variants
22:59:53.785 INFO FilterMutectCalls - Starting pass 3 through the variants
22:59:54.318 INFO FilterMutectCalls - Finished pass 3 through the variants
22:59:54.330 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
22:59:54.331 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
22:59:54.331 INFO ProgressMeter - chr7:13975663 0.0 9356 195323.6
22:59:54.331 INFO ProgressMeter - Traversal complete. Processed 9356 total variants in 0.0 minutes.
22:59:54.347 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 10:59:54 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=251658240
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 LS0886.mutect2.raw.vcf.gz --stats LS0886.mutect2.raw.vcf.gz.stats -O LS0886.mutect2.filtered.vcf.gz
22:59:55.573 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
22:59:55.678 INFO SelectVariants - ------------------------------------------------------------
22:59:55.681 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:59:55.681 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
22:59:55.681 INFO SelectVariants - Executing as ?@nf-55d075341560335644e93ff81c966a30-bae08-zx9sb on Linux v6.12.88 amd64
22:59:55.681 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:59:55.681 INFO SelectVariants - Start Date/Time: June 8, 2026 at 10:59:55 PM GMT
22:59:55.681 INFO SelectVariants - ------------------------------------------------------------
22:59:55.682 INFO SelectVariants - ------------------------------------------------------------
22:59:55.682 INFO SelectVariants - HTSJDK Version: 4.1.0
22:59:55.682 INFO SelectVariants - Picard Version: 3.1.1
22:59:55.682 INFO SelectVariants - Built for Spark Version: 3.5.0
22:59:55.683 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:59:55.683 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:59:55.683 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:59:55.683 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:59:55.683 INFO SelectVariants - Deflater: IntelDeflater
22:59:55.683 INFO SelectVariants - Inflater: IntelInflater
22:59:55.683 INFO SelectVariants - GCS max retries/reopens: 20
22:59:55.683 INFO SelectVariants - Requester pays: disabled
22:59:55.684 INFO SelectVariants - Initializing engine
22:59:55.880 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.xa9ZVmeUpZ/LS0886.mutect2.filtered.vcf.gz
22:59:55.975 INFO SelectVariants - Done initializing engine
22:59:56.014 INFO ProgressMeter - Starting traversal
22:59:56.014 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
22:59:56.093 INFO ProgressMeter - chr7:13979617 0.0 2339 1822597.4
22:59:56.093 INFO ProgressMeter - Traversal complete. Processed 2339 total variants in 0.0 minutes.
22:59:56.103 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 10:59:56 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=310378496
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 LS0886.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0886.mutect2.pass.vcf.gz