18:52:38.735 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
18:52:38.826 INFO Mutect2 - ------------------------------------------------------------
18:52:38.828 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
18:52:38.828 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
18:52:38.828 INFO Mutect2 - Executing as ?@nf-bec0fe191e365942d7bb9cceb4092eea-c81d9-57bmg on Linux v6.12.83 amd64
18:52:38.828 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
18:52:38.828 INFO Mutect2 - Start Date/Time: May 29, 2026 at 6:52:38 PM GMT
18:52:38.828 INFO Mutect2 - ------------------------------------------------------------
18:52:38.828 INFO Mutect2 - ------------------------------------------------------------
18:52:38.830 INFO Mutect2 - HTSJDK Version: 4.1.0
18:52:38.830 INFO Mutect2 - Picard Version: 3.1.1
18:52:38.830 INFO Mutect2 - Built for Spark Version: 3.5.0
18:52:38.830 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:52:38.830 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:52:38.830 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:52:38.832 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:52:38.833 INFO Mutect2 - Deflater: IntelDeflater
18:52:38.833 INFO Mutect2 - Inflater: IntelInflater
18:52:38.833 INFO Mutect2 - GCS max retries/reopens: 20
18:52:38.833 INFO Mutect2 - Requester pays: disabled
18:52:38.833 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.A05fwqfqAh/LS0881.markdup.deduped.nosingletons.bam.bai is older than BAM /tmp/nxf.A05fwqfqAh/LS0881.markdup.deduped.nosingletons.bam
18:52:38.934 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.A05fwqfqAh/af-only-gnomad.hg38.vcf.gz
18:52:39.021 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.A05fwqfqAh/TST500C_manifest.bed
18:52:39.049 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
18:52:39.074 INFO Mutect2 - Done initializing engine
18:52:39.082 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
18:52:39.083 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
18:52:39.083 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
18:52:39.083 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
18:52:39.096 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
18:52:39.108 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
18:52:39.108 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
18:52:39.109 INFO IntelPairHmm - Available threads: 192
18:52:39.109 INFO IntelPairHmm - Requested threads: 4
18:52:39.109 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
18:52:39.140 INFO ProgressMeter - Starting traversal
18:52:39.140 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
18:52:50.343 INFO ProgressMeter - chr1:11204559 0.2 80 428.5
18:53:02.912 INFO ProgressMeter - chr1:15933281 0.4 140 353.4
18:53:13.122 INFO ProgressMeter - chr1:18747566 0.6 190 335.5
18:53:23.611 INFO ProgressMeter - chr1:36473433 0.7 260 350.8
18:53:34.118 INFO ProgressMeter - chr1:45332916 0.9 330 360.1
18:53:44.714 INFO ProgressMeter - chr1:64866864 1.1 410 375.1
18:53:56.603 INFO ProgressMeter - chr1:119915462 1.3 510 395.0
18:54:07.659 INFO ProgressMeter - chr1:156872276 1.5 580 393.1
18:54:18.610 INFO ProgressMeter - chr1:158649901 1.7 640 386.0
18:54:30.097 INFO ProgressMeter - chr1:179108316 1.8 720 389.3
18:54:40.533 INFO ProgressMeter - chr1:204534879 2.0 810 400.4
18:54:50.928 INFO ProgressMeter - chr1:241513601 2.2 910 414.3
18:55:02.453 INFO ProgressMeter - chr10:32011450 2.4 1020 427.0
18:55:13.338 INFO ProgressMeter - chr10:43114970 2.6 1090 424.1
18:55:23.857 INFO ProgressMeter - chr10:62091160 2.7 1140 415.3
18:55:34.488 INFO ProgressMeter - chr10:87895240 2.9 1200 410.6
18:55:45.429 INFO ProgressMeter - chr10:110601616 3.1 1310 421.9
18:55:55.800 INFO ProgressMeter - chr10:121517317 3.3 1380 421.0
18:56:06.095 INFO ProgressMeter - chr11:64805168 3.4 1480 429.1
18:56:17.226 INFO ProgressMeter - chr11:69769630 3.6 1580 434.7
18:56:27.607 INFO ProgressMeter - chr11:76451856 3.8 1660 435.9
18:56:37.856 INFO ProgressMeter - chr11:77460651 4.0 1740 437.3
18:56:48.352 INFO ProgressMeter - chr11:108258984 4.2 1830 440.6
18:56:58.500 INFO ProgressMeter - chr11:118482420 4.3 1910 441.9
18:57:09.481 INFO ProgressMeter - chr11:119298356 4.5 1970 437.2
18:57:20.140 INFO ProgressMeter - chr11:128772780 4.7 2050 437.7
18:57:31.506 INFO ProgressMeter - chr12:4372592 4.9 2130 437.1
18:57:42.790 INFO ProgressMeter - chr12:6591914 5.1 2210 436.7
18:57:54.213 INFO ProgressMeter - chr12:11861030 5.3 2270 432.3
18:58:05.093 INFO ProgressMeter - chr12:18313960 5.4 2330 428.9
18:58:16.355 INFO ProgressMeter - chr12:45850934 5.6 2430 432.4
18:58:28.344 INFO ProgressMeter - chr12:49040622 5.8 2490 427.8
18:58:38.521 INFO ProgressMeter - chr12:56087092 6.0 2570 429.1
18:58:48.529 INFO ProgressMeter - chr12:57463997 6.2 2630 427.2
18:58:58.979 INFO ProgressMeter - chr12:68839272 6.3 2720 429.7
18:59:10.633 INFO ProgressMeter - chr12:120999274 6.5 2810 430.7
18:59:22.031 INFO ProgressMeter - chr13:20991270 6.7 2890 430.4
18:59:33.154 INFO ProgressMeter - chr13:28357552 6.9 2990 433.3
18:59:43.221 INFO ProgressMeter - chr13:32332630 7.1 3050 431.5
18:59:54.729 INFO ProgressMeter - chr13:40560421 7.3 3110 428.4
19:00:06.172 INFO ProgressMeter - chr13:102862028 7.5 3220 432.2
19:00:16.725 INFO ProgressMeter - chr14:35403148 7.6 3310 434.0
19:00:27.285 INFO ProgressMeter - chr14:81108547 7.8 3420 438.3
19:00:37.645 INFO ProgressMeter - chr15:32722800 8.0 3500 438.9
19:00:48.178 INFO ProgressMeter - chr15:41698861 8.2 3560 436.8
19:00:58.762 INFO ProgressMeter - chr15:49430715 8.3 3620 434.7
19:01:09.704 INFO ProgressMeter - chr15:87978987 8.5 3700 434.8
19:01:20.123 INFO ProgressMeter - chr15:90769131 8.7 3790 436.5
19:01:31.184 INFO ProgressMeter - chr15:98957059 8.9 3870 436.4
19:01:41.414 INFO ProgressMeter - chr16:2622690 9.0 3970 439.3
19:01:52.580 INFO ProgressMeter - chr16:3850295 9.2 4040 438.0
19:02:03.315 INFO ProgressMeter - chr16:23634860 9.4 4110 437.1
19:02:13.877 INFO ProgressMeter - chr16:68808691 9.6 4200 438.5
19:02:25.467 INFO ProgressMeter - chr16:72958154 9.8 4250 434.9
19:02:37.623 INFO ProgressMeter - chr16:89283733 10.0 4330 434.1
19:02:47.853 INFO ProgressMeter - chr17:7675458 10.1 4430 436.7
19:02:58.209 INFO ProgressMeter - chr17:16126080 10.3 4530 439.0
19:03:08.633 INFO ProgressMeter - chr17:31994562 10.5 4640 442.3
19:03:19.302 INFO ProgressMeter - chr17:39723373 10.7 4710 441.5
19:03:29.885 INFO ProgressMeter - chr17:42291970 10.8 4790 441.6
19:03:41.796 INFO ProgressMeter - chr17:43094133 11.0 4870 441.0
19:03:52.080 INFO ProgressMeter - chr17:43540026 11.2 4930 439.6
19:04:03.433 INFO ProgressMeter - chr17:58357164 11.4 4990 437.5
19:04:13.820 INFO ProgressMeter - chr17:60600413 11.6 5070 437.9
19:04:24.002 INFO ProgressMeter - chr17:65541453 11.7 5130 436.7
19:04:34.308 INFO ProgressMeter - chr18:1127945 11.9 5220 437.9
19:04:44.565 INFO ProgressMeter - chr18:51054779 12.1 5300 438.4
19:04:55.116 INFO ProgressMeter - chr19:2229783 12.3 5410 441.0
19:05:05.455 INFO ProgressMeter - chr19:7132156 12.4 5500 442.2
19:05:16.153 INFO ProgressMeter - chr19:11019589 12.6 5590 443.1
19:05:27.076 INFO ProgressMeter - chr19:15191958 12.8 5670 443.0
19:05:37.298 INFO ProgressMeter - chr19:29815169 13.0 5770 444.9
19:05:48.065 INFO ProgressMeter - chr19:40251088 13.1 5870 446.4
19:05:58.842 INFO ProgressMeter - chr19:42293254 13.3 5950 446.4
19:06:08.938 INFO ProgressMeter - chr19:45424075 13.5 6050 448.3
19:06:19.620 INFO ProgressMeter - chr2:17764895 13.7 6140 449.0
19:06:30.149 INFO ProgressMeter - chr2:25753532 13.9 6200 447.6
19:06:41.518 INFO ProgressMeter - chr2:29225483 14.0 6250 445.2
19:06:52.369 INFO ProgressMeter - chr2:42261119 14.2 6300 443.0
19:07:03.262 INFO ProgressMeter - chr2:47476365 14.4 6360 441.6
19:07:13.771 INFO ProgressMeter - chr2:96253806 14.6 6440 441.8
19:07:23.918 INFO ProgressMeter - chr2:108766891 14.7 6510 441.5
19:07:34.954 INFO ProgressMeter - chr2:113222575 14.9 6570 440.0
19:07:46.582 INFO ProgressMeter - chr2:113231622 15.1 6620 437.7
19:07:56.769 INFO ProgressMeter - chr2:140234784 15.3 6690 437.4
19:08:07.832 INFO ProgressMeter - chr2:140950262 15.5 6770 437.4
19:08:18.635 INFO ProgressMeter - chr2:191032956 15.7 6850 437.5
19:08:29.239 INFO ProgressMeter - chr2:211619175 15.8 6940 438.3
19:08:40.273 INFO ProgressMeter - chr2:222204065 16.0 7010 437.6
19:08:51.347 INFO ProgressMeter - chr2:222214858 16.2 7060 435.7
19:09:01.361 INFO ProgressMeter - chr2:224505954 16.4 7110 434.3
19:09:13.130 INFO ProgressMeter - chr20:32435030 16.6 7190 434.0
19:09:23.461 INFO ProgressMeter - chr20:41118167 16.7 7260 433.7
19:09:35.657 INFO ProgressMeter - chr20:47647071 16.9 7320 432.1
19:09:46.651 INFO ProgressMeter - chr20:58854464 17.1 7360 429.8
19:09:58.391 INFO ProgressMeter - chr21:38471432 17.3 7440 429.5
19:10:09.270 INFO ProgressMeter - chr21:41493956 17.5 7500 428.5
19:10:21.465 INFO ProgressMeter - chr21:41507760 17.7 7550 426.4
19:10:32.231 INFO ProgressMeter - chr22:23292003 17.9 7640 427.2
19:10:43.089 INFO ProgressMeter - chr22:29636749 18.1 7760 429.5
19:10:53.640 INFO ProgressMeter - chr3:10035171 18.2 7840 429.8
19:11:05.153 INFO ProgressMeter - chr3:12358931 18.4 7920 429.7
19:11:15.176 INFO ProgressMeter - chr3:12370654 18.6 7970 428.5
19:11:25.883 INFO ProgressMeter - chr3:12600386 18.8 8030 427.6
19:11:35.953 INFO ProgressMeter - chr3:47056819 18.9 8120 428.6
19:11:47.403 INFO ProgressMeter - chr3:49897518 19.1 8200 428.5
19:11:57.777 INFO ProgressMeter - chr3:69959271 19.3 8280 428.8
19:12:07.872 INFO ProgressMeter - chr3:128485725 19.5 8360 429.2
19:12:18.664 INFO ProgressMeter - chr3:138704226 19.7 8440 429.3
19:12:28.991 INFO ProgressMeter - chr3:170273284 19.8 8530 430.1
19:12:40.220 INFO ProgressMeter - chr3:183527843 20.0 8610 430.1
19:12:51.305 INFO ProgressMeter - chr3:189631514 20.2 8680 429.6
19:13:02.018 INFO ProgressMeter - chr4:1806130 20.4 8780 430.8
19:13:13.512 INFO ProgressMeter - chr4:54274529 20.6 8870 431.2
19:13:24.885 INFO ProgressMeter - chr4:55121095 20.8 8960 431.5
19:13:35.162 INFO ProgressMeter - chr4:105233941 20.9 9050 432.3
19:13:45.500 INFO ProgressMeter - chr4:122855984 21.1 9110 431.6
19:13:56.396 INFO ProgressMeter - chr4:186609799 21.3 9210 432.6
19:14:07.133 INFO ProgressMeter - chr5:230959 21.5 9270 431.8
19:14:17.443 INFO ProgressMeter - chr5:44355187 21.6 9370 433.0
19:14:28.171 INFO ProgressMeter - chr5:80778718 21.8 9480 434.5
19:14:39.013 INFO ProgressMeter - chr5:122403791 22.0 9570 435.0
19:14:50.189 INFO ProgressMeter - chr5:142682759 22.2 9660 435.4
19:15:00.799 INFO ProgressMeter - chr5:150143203 22.4 9740 435.6
19:15:11.257 INFO ProgressMeter - chr5:177093280 22.5 9820 435.8
19:15:22.881 INFO ProgressMeter - chr5:177512759 22.7 9880 434.7
19:15:32.901 INFO ProgressMeter - chr6:20436963 22.9 9960 435.0
19:15:43.842 INFO ProgressMeter - chr6:36680524 23.1 10150 439.8
19:15:54.682 INFO ProgressMeter - chr6:106107113 23.3 10260 441.1
19:16:06.066 INFO ProgressMeter - chr6:117325472 23.4 10320 440.1
19:16:17.648 INFO ProgressMeter - chr6:117340439 23.6 10380 439.1
19:16:28.052 INFO ProgressMeter - chr6:135206139 23.8 10450 438.8
19:16:39.624 INFO ProgressMeter - chr6:135217539 24.0 10510 437.8
19:16:49.735 INFO ProgressMeter - chr6:151808227 24.2 10570 437.2
19:17:00.154 INFO ProgressMeter - chr6:161049680 24.4 10650 437.4
19:17:11.238 INFO ProgressMeter - chr7:13891895 24.5 10760 438.6
19:17:21.547 INFO ProgressMeter - chr7:13934755 24.7 10810 437.5
19:17:31.652 INFO ProgressMeter - chr7:13944888 24.9 10870 437.0
19:17:42.858 INFO ProgressMeter - chr7:13957625 25.1 10920 435.7
19:17:54.016 INFO ProgressMeter - chr7:13971386 25.2 10980 434.9
19:18:04.065 INFO ProgressMeter - chr7:13980717 25.4 11040 434.4
19:18:14.665 INFO ProgressMeter - chr7:41689648 25.6 11100 433.7
19:18:25.906 INFO ProgressMeter - chr7:55168603 25.8 11160 432.9
19:18:37.378 INFO ProgressMeter - chr7:55180605 26.0 11210 431.6
19:18:48.837 INFO ProgressMeter - chr7:86839437 26.2 11290 431.5
19:19:01.018 INFO ProgressMeter - chr7:106869524 26.4 11390 432.0
19:19:11.517 INFO ProgressMeter - chr7:137345130 26.5 11460 431.8
19:19:22.378 INFO ProgressMeter - chr7:148829726 26.7 11570 433.0
19:19:33.282 INFO ProgressMeter - chr7:152221999 26.9 11640 432.7
19:19:43.581 INFO ProgressMeter - chr8:31639983 27.1 11710 432.5
19:19:53.704 INFO ProgressMeter - chr8:37833686 27.2 11780 432.4
19:20:04.280 INFO ProgressMeter - chr8:41947749 27.4 11850 432.2
19:20:14.820 INFO ProgressMeter - chr8:47939549 27.6 11940 432.7
19:20:25.139 INFO ProgressMeter - chr8:89981373 27.8 12040 433.6
19:20:35.243 INFO ProgressMeter - chr8:144512396 27.9 12120 433.9
19:20:45.363 INFO ProgressMeter - chr9:8497240 28.1 12220 434.8
19:20:56.137 INFO ProgressMeter - chr9:84723571 28.3 12330 435.9
19:21:07.112 INFO ProgressMeter - chr9:84861952 28.5 12380 434.9
19:21:18.400 INFO ProgressMeter - chr9:84873890 28.7 12430 433.8
19:21:28.827 INFO ProgressMeter - chr9:85024829 28.8 12470 432.6
19:21:39.321 INFO ProgressMeter - chr9:95508159 29.0 12550 432.7
19:21:49.562 INFO ProgressMeter - chr9:130887452 29.2 12620 432.6
19:22:00.049 INFO ProgressMeter - chr9:136670167 29.3 12700 432.7
19:22:10.877 INFO ProgressMeter - chrX:45078398 29.5 12790 433.1
19:22:22.358 INFO ProgressMeter - chrX:49038967 29.7 12890 433.7
19:22:34.236 INFO ProgressMeter - chrX:64191377 29.9 12960 433.2
19:22:44.510 INFO ProgressMeter - chrX:71134355 30.1 13050 433.7
19:22:55.479 INFO ProgressMeter - chrX:77683709 30.3 13140 434.1
19:23:05.805 INFO ProgressMeter - chrX:130012576 30.4 13240 434.9
19:23:12.516 INFO Mutect2 - 911053 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
166 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
911219 total reads filtered out of 60604347 reads processed
19:23:12.516 INFO ProgressMeter - chrY:21207343 30.6 13310 435.6
19:23:12.516 INFO ProgressMeter - Traversal complete. Processed 13310 total regions in 30.6 minutes.
19:23:12.528 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 2.405715974
19:23:12.528 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 16.351845837000003
19:23:12.528 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.63 sec
19:23:12.529 INFO Mutect2 - Shutting down engine
[May 29, 2026 at 7:23:12 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 30.56 minutes.
Runtime.totalMemory()=675807232
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar Mutect2 -R hg38.fa -I LS0881.markdup.deduped.nosingletons.bam --tumor-sample LS0881 -L TST500C_manifest.bed -O LS0881.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 20 --germline-resource af-only-gnomad.hg38.vcf.gz
19:23:13.683 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
19:23:13.770 INFO FilterMutectCalls - ------------------------------------------------------------
19:23:13.772 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:23:13.772 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
19:23:13.772 INFO FilterMutectCalls - Executing as ?@nf-bec0fe191e365942d7bb9cceb4092eea-c81d9-57bmg on Linux v6.12.83 amd64
19:23:13.772 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:23:13.772 INFO FilterMutectCalls - Start Date/Time: May 29, 2026 at 7:23:13 PM GMT
19:23:13.772 INFO FilterMutectCalls - ------------------------------------------------------------
19:23:13.772 INFO FilterMutectCalls - ------------------------------------------------------------
19:23:13.773 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
19:23:13.773 INFO FilterMutectCalls - Picard Version: 3.1.1
19:23:13.773 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
19:23:13.773 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:23:13.773 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:23:13.773 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:23:13.774 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:23:13.774 INFO FilterMutectCalls - Deflater: IntelDeflater
19:23:13.774 INFO FilterMutectCalls - Inflater: IntelInflater
19:23:13.774 INFO FilterMutectCalls - GCS max retries/reopens: 20
19:23:13.774 INFO FilterMutectCalls - Requester pays: disabled
19:23:13.774 INFO FilterMutectCalls - Initializing engine
19:23:13.872 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.A05fwqfqAh/LS0881.mutect2.raw.vcf.gz
19:23:13.920 INFO FilterMutectCalls - Done initializing engine
19:23:13.957 INFO ProgressMeter - Starting traversal
19:23:13.957 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:23:13.958 INFO FilterMutectCalls - Starting pass 0 through the variants
19:23:14.840 INFO FilterMutectCalls - Finished pass 0 through the variants
19:23:18.586 INFO FilterMutectCalls - Starting pass 1 through the variants
19:23:19.693 INFO FilterMutectCalls - Finished pass 1 through the variants
19:23:20.451 INFO FilterMutectCalls - Starting pass 2 through the variants
19:23:21.529 INFO FilterMutectCalls - Finished pass 2 through the variants
19:23:21.530 INFO FilterMutectCalls - Starting pass 3 through the variants
19:23:22.477 INFO FilterMutectCalls - Finished pass 3 through the variants
19:23:22.484 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
19:23:22.484 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
19:23:22.485 INFO ProgressMeter - chr7:13970244 0.1 5244 36899.3
19:23:22.485 INFO ProgressMeter - Traversal complete. Processed 5244 total variants in 0.1 minutes.
19:23:22.495 INFO FilterMutectCalls - Shutting down engine
[May 29, 2026 at 7:23:22 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=806354944
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar FilterMutectCalls -R hg38.fa -V LS0881.mutect2.raw.vcf.gz --stats LS0881.mutect2.raw.vcf.gz.stats -O LS0881.mutect2.filtered.vcf.gz
19:23:23.635 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
19:23:23.723 INFO SelectVariants - ------------------------------------------------------------
19:23:23.725 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
19:23:23.725 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
19:23:23.725 INFO SelectVariants - Executing as ?@nf-bec0fe191e365942d7bb9cceb4092eea-c81d9-57bmg on Linux v6.12.83 amd64
19:23:23.725 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
19:23:23.726 INFO SelectVariants - Start Date/Time: May 29, 2026 at 7:23:23 PM GMT
19:23:23.726 INFO SelectVariants - ------------------------------------------------------------
19:23:23.726 INFO SelectVariants - ------------------------------------------------------------
19:23:23.726 INFO SelectVariants - HTSJDK Version: 4.1.0
19:23:23.726 INFO SelectVariants - Picard Version: 3.1.1
19:23:23.726 INFO SelectVariants - Built for Spark Version: 3.5.0
19:23:23.727 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:23:23.727 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:23:23.727 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:23:23.727 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:23:23.727 INFO SelectVariants - Deflater: IntelDeflater
19:23:23.727 INFO SelectVariants - Inflater: IntelInflater
19:23:23.727 INFO SelectVariants - GCS max retries/reopens: 20
19:23:23.727 INFO SelectVariants - Requester pays: disabled
19:23:23.727 INFO SelectVariants - Initializing engine
19:23:23.819 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.A05fwqfqAh/LS0881.mutect2.filtered.vcf.gz
19:23:23.862 INFO SelectVariants - Done initializing engine
19:23:23.889 INFO ProgressMeter - Starting traversal
19:23:23.889 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
19:23:23.941 INFO ProgressMeter - chr6:151807942 0.0 1311 1573200.0
19:23:23.941 INFO ProgressMeter - Traversal complete. Processed 1311 total variants in 0.0 minutes.
19:23:23.951 INFO SelectVariants - Shutting down engine
[May 29, 2026 at 7:23:23 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=567803904
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 -Xmx24g -XX:+UseParallelGC -jar /gatk/gatk-package-4.5.0.0-local.jar SelectVariants -R hg38.fa -V LS0881.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0881.mutect2.pass.vcf.gz