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/LS0901/LS0901_tumor.bam
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/d3/90ff9cd0838e558429d3a67b8380f9/.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/d3/90ff9cd0838e558429d3a67b8380f9/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0901/LS0901_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:16.814 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
22:44:16.942 INFO Mutect2 - ------------------------------------------------------------
22:44:16.945 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:16.945 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:16.945 INFO Mutect2 - Executing as ?@nf-d390ff9cd0838e558429d3a67b8380f9-4f610-d8n6j on Linux v6.12.88 amd64
22:44:16.946 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:16.946 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:16 PM GMT
22:44:16.946 INFO Mutect2 - ------------------------------------------------------------
22:44:16.946 INFO Mutect2 - ------------------------------------------------------------
22:44:16.947 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:16.947 INFO Mutect2 - Picard Version: 3.1.1
22:44:16.947 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:16.947 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:16.947 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:16.947 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:16.947 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:16.948 INFO Mutect2 - Deflater: IntelDeflater
22:44:16.948 INFO Mutect2 - Inflater: IntelInflater
22:44:16.948 INFO Mutect2 - GCS max retries/reopens: 20
22:44:16.948 INFO Mutect2 - Requester pays: disabled
22:44:16.948 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.jjWVPf1sjl/LS0901_tumor.bam.bai is older than BAM /tmp/nxf.jjWVPf1sjl/LS0901_tumor.bam
22:44:17.136 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.jjWVPf1sjl/af-only-gnomad.hg38.vcf.gz
22:44:17.261 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.jjWVPf1sjl/TST500C_manifest.bed
22:44:17.302 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:17.339 INFO Mutect2 - Done initializing engine
22:44:17.351 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
22:44:17.353 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
22:44:17.354 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:17.354 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:17.364 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
22:44:17.373 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:17.373 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:17.373 INFO IntelPairHmm - Available threads: 384
22:44:17.373 INFO IntelPairHmm - Requested threads: 4
22:44:17.373 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:17.407 INFO ProgressMeter - Starting traversal
22:44:17.407 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:27.740 INFO ProgressMeter - chr1:9721125 0.2 50 290.4
22:44:38.458 INFO ProgressMeter - chr1:11157150 0.4 110 313.5
22:44:48.681 INFO ProgressMeter - chr1:11258550 0.5 170 326.2
22:45:01.658 INFO ProgressMeter - chr1:15931286 0.7 220 298.3
22:45:13.216 INFO ProgressMeter - chr1:15935211 0.9 260 279.5
22:45:23.802 INFO ProgressMeter - chr1:18735630 1.1 320 289.2
22:45:36.811 INFO ProgressMeter - chr1:18748694 1.3 360 272.0
22:45:47.108 INFO ProgressMeter - chr1:26775091 1.5 420 280.9
22:45:57.965 INFO ProgressMeter - chr1:36473508 1.7 480 286.4
22:46:08.272 INFO ProgressMeter - chr1:39900272 1.8 530 286.8
22:46:18.579 INFO ProgressMeter - chr1:45332207 2.0 590 292.1
22:46:29.379 INFO ProgressMeter - chr1:50968783 2.2 660 300.1
22:46:40.481 INFO ProgressMeter - chr1:64879065 2.4 730 306.1
22:46:51.294 INFO ProgressMeter - chr1:114711487 2.6 810 315.8
22:47:03.400 INFO ProgressMeter - chr1:119514157 2.8 870 314.5
22:47:15.038 INFO ProgressMeter - chr1:119937280 3.0 920 310.8
22:47:25.260 INFO ProgressMeter - chr1:156866908 3.1 990 316.2
22:47:36.215 INFO ProgressMeter - chr1:156875521 3.3 1030 310.9
22:47:47.823 INFO ProgressMeter - chr1:158639868 3.5 1080 308.0
22:47:58.305 INFO ProgressMeter - chr1:158685141 3.7 1140 309.6
22:48:08.458 INFO ProgressMeter - chr1:179107868 3.9 1210 314.2
22:48:18.711 INFO ProgressMeter - chr1:204433791 4.0 1280 318.3
22:48:28.750 INFO ProgressMeter - chr1:204525517 4.2 1340 319.9
22:48:39.918 INFO ProgressMeter - chr1:206479071 4.4 1400 320.0
22:48:51.390 INFO ProgressMeter - chr1:228429800 4.6 1480 324.1
22:49:02.329 INFO ProgressMeter - chr1:243501990 4.7 1530 322.2
22:49:12.728 INFO ProgressMeter - chr1:243512322 4.9 1560 316.9
22:49:24.334 INFO ProgressMeter - chr10:27035385 5.1 1630 318.6
22:49:35.996 INFO ProgressMeter - chr10:32011210 5.3 1690 318.3
22:49:45.999 INFO ProgressMeter - chr10:43109029 5.5 1760 321.4
22:49:57.337 INFO ProgressMeter - chr10:43114970 5.7 1800 317.7
22:50:07.579 INFO ProgressMeter - chr10:43123147 5.8 1840 315.3
22:50:19.568 INFO ProgressMeter - chr10:62092913 6.0 1890 313.1
22:50:31.291 INFO ProgressMeter - chr10:68667163 6.2 1940 311.3
22:50:41.492 INFO ProgressMeter - chr10:87922101 6.4 2000 312.4
22:50:52.869 INFO ProgressMeter - chr10:101770750 6.6 2060 312.5
22:51:03.179 INFO ProgressMeter - chr10:102627173 6.8 2130 315.0
22:51:14.274 INFO ProgressMeter - chr10:112950755 6.9 2190 315.2
22:51:25.637 INFO ProgressMeter - chr10:121481520 7.1 2240 313.9
22:51:37.003 INFO ProgressMeter - chr10:121519977 7.3 2280 311.2
22:51:48.205 INFO ProgressMeter - chr11:8227009 7.5 2340 311.4
22:51:59.410 INFO ProgressMeter - chr11:64368702 7.7 2410 313.0
22:52:09.525 INFO ProgressMeter - chr11:69646179 7.9 2480 315.2
22:52:20.515 INFO ProgressMeter - chr11:69701108 8.1 2540 315.5
22:52:31.379 INFO ProgressMeter - chr11:69771328 8.2 2590 314.6
22:52:45.961 INFO ProgressMeter - chr11:69810318 8.5 2640 311.5
22:52:55.976 INFO ProgressMeter - chr11:69820617 8.6 2690 311.2
22:53:06.156 INFO ProgressMeter - chr11:77339580 8.8 2750 312.1
22:53:18.013 INFO ProgressMeter - chr11:77422651 9.0 2810 311.9
22:53:28.813 INFO ProgressMeter - chr11:101051569 9.2 2890 314.5
22:53:41.844 INFO ProgressMeter - chr11:102322618 9.4 2930 311.5
22:53:53.210 INFO ProgressMeter - chr11:108288978 9.6 3000 312.6
22:54:03.237 INFO ProgressMeter - chr11:118436832 9.8 3080 315.4
22:54:14.438 INFO ProgressMeter - chr11:118491194 10.0 3130 314.6
22:54:25.964 INFO ProgressMeter - chr11:118505326 10.1 3180 313.5
22:54:37.596 INFO ProgressMeter - chr11:119298491 10.3 3240 313.5
22:54:47.818 INFO ProgressMeter - chr11:125638675 10.5 3270 311.2
22:55:02.817 INFO ProgressMeter - chr11:128460328 10.8 3320 308.6
22:55:12.883 INFO ProgressMeter - chr11:128522246 10.9 3360 307.6
22:55:24.168 INFO ProgressMeter - chr11:128813016 11.1 3400 306.0
22:55:34.657 INFO ProgressMeter - chr12:363010 11.3 3460 306.5
22:55:46.074 INFO ProgressMeter - chr12:4373738 11.5 3530 307.6
22:55:56.828 INFO ProgressMeter - chr12:4437023 11.7 3590 308.0
22:56:08.307 INFO ProgressMeter - chr12:6581361 11.8 3650 308.1
22:56:21.473 INFO ProgressMeter - chr12:11752429 12.1 3710 307.4
22:56:34.067 INFO ProgressMeter - chr12:11856865 12.3 3750 305.4
22:56:49.525 INFO ProgressMeter - chr12:11861533 12.5 3790 302.3
22:57:01.418 INFO ProgressMeter - chr12:11866386 12.7 3830 300.8
22:57:13.603 INFO ProgressMeter - chr12:11884435 12.9 3860 298.4
22:57:23.715 INFO ProgressMeter - chr12:18594492 13.1 3930 299.9
22:57:35.453 INFO ProgressMeter - chr12:31797603 13.3 4000 300.7
22:57:45.944 INFO ProgressMeter - chr12:45851543 13.5 4050 300.5
22:57:57.292 INFO ProgressMeter - chr12:49031230 13.7 4110 300.8
22:58:07.806 INFO ProgressMeter - chr12:49037302 13.8 4140 299.1
22:58:18.467 INFO ProgressMeter - chr12:49043783 14.0 4190 298.9
22:58:29.794 INFO ProgressMeter - chr12:49054348 14.2 4250 299.2
22:58:41.004 INFO ProgressMeter - chr12:56087793 14.4 4330 300.8
22:58:52.352 INFO ProgressMeter - chr12:57091710 14.6 4400 301.7
22:59:02.730 INFO ProgressMeter - chr12:57468148 14.8 4450 301.6
22:59:13.004 INFO ProgressMeter - chr12:57751579 14.9 4510 302.1
22:59:24.067 INFO ProgressMeter - chr12:68838080 15.1 4570 302.4
22:59:34.178 INFO ProgressMeter - chr12:111418522 15.3 4630 303.0
22:59:45.168 INFO ProgressMeter - chr12:120097262 15.5 4700 304.0
22:59:55.478 INFO ProgressMeter - chr12:132639177 15.6 4760 304.5
23:00:06.609 INFO ProgressMeter - chr12:132680176 15.8 4830 305.3
23:00:18.116 INFO ProgressMeter - chr13:21676321 16.0 4880 304.8
23:00:28.127 INFO ProgressMeter - chr13:26404050 16.2 4950 306.0
23:00:39.330 INFO ProgressMeter - chr13:28345489 16.4 5020 306.7
23:00:49.447 INFO ProgressMeter - chr13:28387922 16.5 5050 305.4
23:01:00.298 INFO ProgressMeter - chr13:32317658 16.7 5090 304.5
23:01:11.027 INFO ProgressMeter - chr13:32338129 16.9 5130 303.7
23:01:21.904 INFO ProgressMeter - chr13:32356507 17.1 5180 303.4
23:01:32.660 INFO ProgressMeter - chr13:48342597 17.3 5240 303.7
23:01:42.905 INFO ProgressMeter - chr13:72781304 17.4 5310 304.7
23:01:53.537 INFO ProgressMeter - chr13:102854286 17.6 5380 305.6
23:02:04.830 INFO ProgressMeter - chr13:109784311 17.8 5440 305.8
23:02:19.334 INFO ProgressMeter - chr14:23307835 18.0 5510 305.6
23:02:29.526 INFO ProgressMeter - chr14:37591663 18.2 5580 306.6
23:02:40.167 INFO ProgressMeter - chr14:65076474 18.4 5640 306.9
23:02:52.068 INFO ProgressMeter - chr14:81143809 18.6 5710 307.4
23:03:03.037 INFO ProgressMeter - chr14:95116451 18.8 5760 307.0
23:03:13.123 INFO ProgressMeter - chr14:104770339 18.9 5820 307.5
23:03:27.352 INFO ProgressMeter - chr15:34347980 19.2 5870 306.3
23:03:37.626 INFO ProgressMeter - chr15:40731053 19.3 5920 306.1
23:03:48.599 INFO ProgressMeter - chr15:41734520 19.5 5970 305.8
23:04:01.597 INFO ProgressMeter - chr15:41766697 19.7 6020 305.0
23:04:12.315 INFO ProgressMeter - chr15:49469984 19.9 6090 305.8
23:04:24.487 INFO ProgressMeter - chr15:87978009 20.1 6160 306.2
23:04:34.575 INFO ProgressMeter - chr15:89276709 20.3 6220 306.6
23:04:45.120 INFO ProgressMeter - chr15:90754809 20.5 6290 307.4
23:04:55.788 INFO ProgressMeter - chr15:92953458 20.6 6350 307.7
23:05:06.095 INFO ProgressMeter - chr15:98891550 20.8 6410 308.0
23:05:18.604 INFO ProgressMeter - chr16:2050398 21.0 6480 308.3
23:05:28.940 INFO ProgressMeter - chr16:2165877 21.2 6550 309.1
23:05:38.985 INFO ProgressMeter - chr16:3589588 21.4 6630 310.4
23:05:52.302 INFO ProgressMeter - chr16:3728590 21.6 6680 309.5
23:06:02.838 INFO ProgressMeter - chr16:3850295 21.8 6740 309.8
23:06:13.731 INFO ProgressMeter - chr16:9938090 21.9 6790 309.5
23:06:24.054 INFO ProgressMeter - chr16:23621386 22.1 6850 309.8
23:06:34.507 INFO ProgressMeter - chr16:31135152 22.3 6910 310.1
23:06:45.132 INFO ProgressMeter - chr16:56844497 22.5 6980 310.7
23:06:56.139 INFO ProgressMeter - chr16:72787162 22.6 7040 310.9
23:07:07.143 INFO ProgressMeter - chr16:72795679 22.8 7080 310.1
23:07:20.007 INFO ProgressMeter - chr16:72798716 23.0 7110 308.5
23:07:31.141 INFO ProgressMeter - chr16:81889170 23.2 7160 308.2
23:07:43.102 INFO ProgressMeter - chr16:89281124 23.4 7230 308.6
23:07:53.216 INFO ProgressMeter - chr16:89284602 23.6 7260 307.7
23:08:03.322 INFO ProgressMeter - chr16:89791925 23.8 7330 308.4
23:08:13.920 INFO ProgressMeter - chr17:7673750 23.9 7400 309.1
23:08:24.768 INFO ProgressMeter - chr17:8073655 24.1 7460 309.3
23:08:36.512 INFO ProgressMeter - chr17:16070163 24.3 7540 310.1
23:08:46.620 INFO ProgressMeter - chr17:17213762 24.5 7610 310.8
23:08:56.677 INFO ProgressMeter - chr17:31222428 24.7 7680 311.5
23:09:07.258 INFO ProgressMeter - chr17:31357267 24.8 7750 312.1
23:09:18.507 INFO ProgressMeter - chr17:39501248 25.0 7830 313.0
23:09:29.844 INFO ProgressMeter - chr17:39716513 25.2 7900 313.4
23:09:40.364 INFO ProgressMeter - chr17:40396281 25.4 7970 314.0
23:09:50.466 INFO ProgressMeter - chr17:42291970 25.6 8050 315.1
23:10:01.277 INFO ProgressMeter - chr17:43063331 25.7 8130 316.0
23:10:11.667 INFO ProgressMeter - chr17:43092826 25.9 8180 315.8
23:10:22.222 INFO ProgressMeter - chr17:43528181 26.1 8230 315.6
23:10:32.425 INFO ProgressMeter - chr17:43534281 26.3 8270 315.0
23:10:44.115 INFO ProgressMeter - chr17:43540725 26.4 8320 314.6
23:10:56.219 INFO ProgressMeter - chr17:43544110 26.6 8350 313.4
23:11:07.039 INFO ProgressMeter - chr17:49601890 26.8 8410 313.5
23:11:17.752 INFO ProgressMeter - chr17:59893794 27.0 8470 313.6
23:11:29.644 INFO ProgressMeter - chr17:60600413 27.2 8540 313.9
23:11:40.500 INFO ProgressMeter - chr17:61849127 27.4 8600 314.0
23:11:50.762 INFO ProgressMeter - chr17:65558436 27.6 8660 314.3
23:12:01.839 INFO ProgressMeter - chr17:80857808 27.7 8740 315.1
23:12:12.178 INFO ProgressMeter - chr18:22172164 27.9 8810 315.6
23:12:23.631 INFO ProgressMeter - chr18:44951325 28.1 8880 316.0
23:12:34.712 INFO ProgressMeter - chr18:51076636 28.3 8930 315.7
23:12:45.725 INFO ProgressMeter - chr19:1221947 28.5 9010 316.5
23:12:56.517 INFO ProgressMeter - chr19:2226285 28.7 9090 317.3
23:13:07.552 INFO ProgressMeter - chr19:5212407 28.8 9170 318.0
23:13:17.853 INFO ProgressMeter - chr19:7120618 29.0 9240 318.5
23:13:29.275 INFO ProgressMeter - chr19:10146461 29.2 9310 318.9
23:13:39.813 INFO ProgressMeter - chr19:10499830 29.4 9370 319.0
23:13:50.919 INFO ProgressMeter - chr19:12940406 29.6 9450 319.7
23:14:00.960 INFO ProgressMeter - chr19:15167404 29.7 9500 319.6
23:14:12.343 INFO ProgressMeter - chr19:15191996 29.9 9560 319.6
23:14:23.296 INFO ProgressMeter - chr19:17834962 30.1 9630 320.0
23:14:34.681 INFO ProgressMeter - chr19:29815213 30.3 9720 320.9
23:14:45.264 INFO ProgressMeter - chr19:35720146 30.5 9780 321.0
23:14:56.760 INFO ProgressMeter - chr19:35733761 30.7 9850 321.3
23:15:07.303 INFO ProgressMeter - chr19:41219197 30.8 9920 321.7
23:15:19.247 INFO ProgressMeter - chr19:41260682 31.0 9970 321.3
23:15:29.328 INFO ProgressMeter - chr19:42292954 31.2 10030 321.5
23:15:40.272 INFO ProgressMeter - chr19:45370467 31.4 10100 321.8
23:15:52.598 INFO ProgressMeter - chr19:50402260 31.6 10180 322.3
23:16:05.907 INFO ProgressMeter - chr2:15940616 31.8 10260 322.6
23:16:17.831 INFO ProgressMeter - chr2:17766645 32.0 10320 322.4
23:16:29.059 INFO ProgressMeter - chr2:25281739 32.2 10380 322.4
23:16:40.768 INFO ProgressMeter - chr2:25799383 32.4 10430 322.0
23:16:52.393 INFO ProgressMeter - chr2:29223994 32.6 10480 321.6
23:17:02.776 INFO ProgressMeter - chr2:29226842 32.8 10510 320.9
23:17:15.320 INFO ProgressMeter - chr2:42169348 33.0 10570 320.6
23:17:26.616 INFO ProgressMeter - chr2:47373525 33.2 10630 320.6
23:17:37.369 INFO ProgressMeter - chr2:47476416 33.3 10670 320.1
23:17:47.858 INFO ProgressMeter - chr2:47805627 33.5 10720 319.9
23:17:58.337 INFO ProgressMeter - chr2:61498743 33.7 10800 320.6
23:18:08.342 INFO ProgressMeter - chr2:98539526 33.8 10830 320.0
23:18:20.135 INFO ProgressMeter - chr2:108764657 34.0 10910 320.5
23:18:30.753 INFO ProgressMeter - chr2:111125806 34.2 10970 320.5
23:18:41.473 INFO ProgressMeter - chr2:111127848 34.4 10990 319.5
23:18:52.732 INFO ProgressMeter - chr2:113222257 34.6 11030 318.9
23:19:03.995 INFO ProgressMeter - chr2:113225887 34.8 11060 318.0
23:19:14.386 INFO ProgressMeter - chr2:113228818 34.9 11090 317.3
23:19:25.144 INFO ProgressMeter - chr2:113233057 35.1 11130 316.8
23:19:35.370 INFO ProgressMeter - chr2:113242688 35.3 11170 316.4
23:19:45.972 INFO ProgressMeter - chr2:140323891 35.5 11240 316.8
23:19:56.190 INFO ProgressMeter - chr2:140541049 35.6 11310 317.3
23:20:07.404 INFO ProgressMeter - chr2:141013612 35.8 11380 317.6
23:20:17.713 INFO ProgressMeter - chr2:172558706 36.0 11430 317.5
23:20:28.731 INFO ProgressMeter - chr2:189867797 36.2 11490 317.5
23:20:39.238 INFO ProgressMeter - chr2:197408481 36.4 11560 317.9
23:20:49.998 INFO ProgressMeter - chr2:211383889 36.5 11630 318.3
23:21:00.417 INFO ProgressMeter - chr2:219567279 36.7 11700 318.7
23:21:12.434 INFO ProgressMeter - chr2:222202360 36.9 11730 317.7
23:21:24.035 INFO ProgressMeter - chr2:222206102 37.1 11770 317.2
23:21:36.165 INFO ProgressMeter - chr2:222210912 37.3 11810 316.5
23:21:48.400 INFO ProgressMeter - chr2:222215413 37.5 11850 315.9
23:22:00.002 INFO ProgressMeter - chr2:222218759 37.7 11880 315.0
23:22:10.273 INFO ProgressMeter - chr2:222298547 37.9 11920 314.7
23:22:22.564 INFO ProgressMeter - chr2:226797293 38.1 11980 314.6
23:22:32.623 INFO ProgressMeter - chr20:15144325 38.3 12030 314.5
23:22:45.133 INFO ProgressMeter - chr20:32436135 38.5 12080 314.1
23:22:55.967 INFO ProgressMeter - chr20:40858433 38.6 12150 314.4
23:23:05.981 INFO ProgressMeter - chr20:42315721 38.8 12220 314.9
23:23:16.224 INFO ProgressMeter - chr20:47647273 39.0 12280 315.0
23:23:26.585 INFO ProgressMeter - chr20:56370156 39.2 12320 314.7
23:23:36.664 INFO ProgressMeter - chr20:58891760 39.3 12370 314.6
23:23:46.734 INFO ProgressMeter - chr21:38380765 39.5 12430 314.8
23:23:58.500 INFO ProgressMeter - chr21:38471196 39.7 12480 314.5
23:24:11.754 INFO ProgressMeter - chr21:41489856 39.9 12530 314.0
23:24:25.277 INFO ProgressMeter - chr21:41492362 40.1 12550 312.7
23:24:36.030 INFO ProgressMeter - chr21:41500500 40.3 12590 312.3
23:24:47.355 INFO ProgressMeter - chr21:41504793 40.5 12630 311.9
23:24:57.766 INFO ProgressMeter - chr21:43094704 40.7 12670 311.5
23:25:08.069 INFO ProgressMeter - chr22:21788255 40.8 12740 311.9
23:25:23.590 INFO ProgressMeter - chr22:23291470 41.1 12800 311.4
23:25:34.107 INFO ProgressMeter - chr22:28711907 41.3 12860 311.5
23:25:44.160 INFO ProgressMeter - chr22:29282736 41.4 12920 311.7
23:25:57.540 INFO ProgressMeter - chr22:29292545 41.7 12970 311.3
23:26:08.085 INFO ProgressMeter - chr22:29674834 41.8 13000 310.7
23:26:19.055 INFO ProgressMeter - chr22:41168465 42.0 13070 311.0
23:26:31.068 INFO ProgressMeter - chr3:10060292 42.2 13130 310.9
23:26:43.209 INFO ProgressMeter - chr3:12354147 42.4 13200 311.1
23:26:55.502 INFO ProgressMeter - chr3:12357579 42.6 13230 310.3
23:27:09.663 INFO ProgressMeter - chr3:12360938 42.9 13260 309.3
23:27:21.859 INFO ProgressMeter - chr3:12366009 43.1 13310 309.0
23:27:32.918 INFO ProgressMeter - chr3:12369815 43.3 13340 308.4
23:27:48.962 INFO ProgressMeter - chr3:12373552 43.5 13380 307.4
23:28:00.542 INFO ProgressMeter - chr3:12378035 43.7 13420 307.0
23:28:11.251 INFO ProgressMeter - chr3:12604219 43.9 13480 307.1
23:28:21.997 INFO ProgressMeter - chr3:30691476 44.1 13540 307.2
23:28:33.312 INFO ProgressMeter - chr3:41239273 44.3 13620 307.7
23:28:43.442 INFO ProgressMeter - chr3:47121134 44.4 13670 307.6
23:28:54.115 INFO ProgressMeter - chr3:49685260 44.6 13720 307.5
23:29:06.408 INFO ProgressMeter - chr3:49902679 44.8 13790 307.7
23:29:17.760 INFO ProgressMeter - chr3:52609532 45.0 13860 308.0
23:29:28.241 INFO ProgressMeter - chr3:70977826 45.2 13930 308.3
23:29:38.347 INFO ProgressMeter - chr3:89210054 45.3 13990 308.5
23:29:48.797 INFO ProgressMeter - chr3:128486801 45.5 14060 308.9
23:29:59.974 INFO ProgressMeter - chr3:136398728 45.7 14120 308.9
23:30:10.379 INFO ProgressMeter - chr3:138704441 45.9 14190 309.3
23:30:20.886 INFO ProgressMeter - chr3:142497075 46.1 14260 309.6
23:30:30.950 INFO ProgressMeter - chr3:142566150 46.2 14320 309.8
23:30:41.511 INFO ProgressMeter - chr3:179210184 46.4 14400 310.3
23:30:51.669 INFO ProgressMeter - chr3:183499669 46.6 14470 310.7
23:31:03.996 INFO ProgressMeter - chr3:186047291 46.8 14530 310.6
23:31:15.797 INFO ProgressMeter - chr3:187729286 47.0 14600 310.8
23:31:26.133 INFO ProgressMeter - chr3:196057898 47.1 14660 311.0
23:31:37.056 INFO ProgressMeter - chr4:1805381 47.3 14740 311.4
23:31:48.915 INFO ProgressMeter - chr4:24529715 47.5 14820 311.8
23:32:00.446 INFO ProgressMeter - chr4:54267287 47.7 14890 312.0
23:32:12.411 INFO ProgressMeter - chr4:54703731 47.9 14960 312.2
23:32:23.990 INFO ProgressMeter - chr4:54733068 48.1 14990 311.6
23:32:34.666 INFO ProgressMeter - chr4:65351387 48.3 15060 311.9
23:32:45.435 INFO ProgressMeter - chr4:80283144 48.5 15130 312.2
23:32:56.477 INFO ProgressMeter - chr4:105235579 48.7 15190 312.2
23:33:06.831 INFO ProgressMeter - chr4:105241037 48.8 15230 311.9
23:33:17.012 INFO ProgressMeter - chr4:105275659 49.0 15270 311.7
23:33:27.704 INFO ProgressMeter - chr4:142145939 49.2 15350 312.2
23:33:37.891 INFO ProgressMeter - chr4:184419564 49.3 15420 312.5
23:33:48.655 INFO ProgressMeter - chr4:186617782 49.5 15480 312.6
23:33:59.424 INFO ProgressMeter - chr4:186628547 49.7 15520 312.3
23:34:09.850 INFO ProgressMeter - chr4:186709241 49.9 15560 312.0
23:34:20.418 INFO ProgressMeter - chr5:35875510 50.1 15620 312.1
23:34:31.493 INFO ProgressMeter - chr5:39074109 50.2 15690 312.3
23:34:42.311 INFO ProgressMeter - chr5:56859713 50.4 15760 312.6
23:34:52.650 INFO ProgressMeter - chr5:58457179 50.6 15820 312.7
23:35:03.652 INFO ProgressMeter - chr5:87333265 50.8 15910 313.4
23:35:15.387 INFO ProgressMeter - chr5:112838945 51.0 15990 313.7
23:35:26.510 INFO ProgressMeter - chr5:112843377 51.2 16030 313.4
23:35:36.831 INFO ProgressMeter - chr5:132591286 51.3 16090 313.5
23:35:48.014 INFO ProgressMeter - chr5:142611936 51.5 16170 313.9
23:35:59.052 INFO ProgressMeter - chr5:142697296 51.7 16220 313.8
23:36:09.352 INFO ProgressMeter - chr5:150086377 51.9 16280 313.9
23:36:22.937 INFO ProgressMeter - chr5:150402236 52.1 16350 313.9
23:36:34.641 INFO ProgressMeter - chr5:177088553 52.3 16420 314.0
23:36:45.196 INFO ProgressMeter - chr5:177093453 52.5 16450 313.6
23:36:56.453 INFO ProgressMeter - chr5:177135666 52.7 16490 313.2
23:37:06.913 INFO ProgressMeter - chr5:177267560 52.8 16530 312.9
23:37:17.371 INFO ProgressMeter - chr5:177515955 53.0 16580 312.8
23:37:27.660 INFO ProgressMeter - chr6:395845 53.2 16650 313.1
23:37:38.546 INFO ProgressMeter - chr6:20469963 53.4 16730 313.6
23:37:49.509 INFO ProgressMeter - chr6:26164817 53.5 16810 314.0
23:38:01.489 INFO ProgressMeter - chr6:30705795 53.7 16880 314.1
23:38:12.830 INFO ProgressMeter - chr6:32198978 53.9 16930 314.0
23:38:23.585 INFO ProgressMeter - chr6:32222670 54.1 16990 314.0
23:38:33.824 INFO ProgressMeter - chr6:36684095 54.3 17050 314.1
23:38:45.042 INFO ProgressMeter - chr6:43780730 54.5 17140 314.7
23:38:57.098 INFO ProgressMeter - chr6:106105555 54.7 17210 314.8
23:39:07.846 INFO ProgressMeter - chr6:117310079 54.8 17270 314.9
23:39:21.668 INFO ProgressMeter - chr6:117321887 55.1 17310 314.3
23:39:32.409 INFO ProgressMeter - chr6:117326618 55.3 17350 314.0
23:39:44.055 INFO ProgressMeter - chr6:117331487 55.4 17400 313.8
23:39:54.524 INFO ProgressMeter - chr6:117337711 55.6 17450 313.7
23:40:05.970 INFO ProgressMeter - chr6:117362840 55.8 17500 313.6
23:40:17.280 INFO ProgressMeter - chr6:135203625 56.0 17570 313.8
23:40:32.105 INFO ProgressMeter - chr6:135208764 56.2 17610 313.1
23:40:46.870 INFO ProgressMeter - chr6:135212428 56.5 17640 312.3
23:41:03.778 INFO ProgressMeter - chr6:135215119 56.8 17660 311.1
23:41:15.192 INFO ProgressMeter - chr6:137875994 57.0 17710 310.9
23:41:26.417 INFO ProgressMeter - chr6:149695072 57.2 17760 310.8
23:41:37.647 INFO ProgressMeter - chr6:151944269 57.3 17810 310.6
23:41:49.045 INFO ProgressMeter - chr6:157174909 57.5 17870 310.6
23:41:59.804 INFO ProgressMeter - chr6:161049159 57.7 17920 310.5
23:42:09.840 INFO ProgressMeter - chr6:161716075 57.9 17980 310.7
23:42:20.558 INFO ProgressMeter - chr7:2945817 58.1 18050 310.9
23:42:31.525 INFO ProgressMeter - chr7:13894766 58.2 18120 311.2
23:42:44.171 INFO ProgressMeter - chr7:13911237 58.4 18160 310.7
23:42:55.546 INFO ProgressMeter - chr7:13935648 58.6 18200 310.4
23:43:07.827 INFO ProgressMeter - chr7:13942207 58.8 18250 310.2
23:43:18.386 INFO ProgressMeter - chr7:13946659 59.0 18280 309.7
23:43:31.217 INFO ProgressMeter - chr7:13950554 59.2 18320 309.3
23:43:41.223 INFO ProgressMeter - chr7:13952798 59.4 18340 308.8
23:43:53.473 INFO ProgressMeter - chr7:13956244 59.6 18380 308.4
23:44:05.143 INFO ProgressMeter - chr7:13960191 59.8 18420 308.0
23:44:17.239 INFO ProgressMeter - chr7:13964910 60.0 18460 307.7
23:44:30.130 INFO ProgressMeter - chr7:13970675 60.2 18510 307.4
23:44:40.521 INFO ProgressMeter - chr7:13975116 60.4 18550 307.2
23:44:51.032 INFO ProgressMeter - chr7:13977794 60.6 18570 306.6
23:45:03.228 INFO ProgressMeter - chr7:13981662 60.8 18610 306.3
23:45:15.233 INFO ProgressMeter - chr7:13985655 61.0 18640 305.8
23:45:25.918 INFO ProgressMeter - chr7:13989115 61.1 18660 305.2
23:45:36.858 INFO ProgressMeter - chr7:55142422 61.3 18720 305.3
23:45:48.239 INFO ProgressMeter - chr7:55161615 61.5 18760 305.0
23:45:59.865 INFO ProgressMeter - chr7:55168847 61.7 18790 304.5
23:46:10.327 INFO ProgressMeter - chr7:55172981 61.9 18810 304.0
23:46:21.280 INFO ProgressMeter - chr7:55177499 62.1 18840 303.6
23:46:32.438 INFO ProgressMeter - chr7:55180687 62.3 18870 303.1
23:46:43.095 INFO ProgressMeter - chr7:78135019 62.4 18920 303.1
23:46:54.429 INFO ProgressMeter - chr7:86765299 62.6 18990 303.3
23:47:06.169 INFO ProgressMeter - chr7:92826463 62.8 19060 303.4
23:47:16.392 INFO ProgressMeter - chr7:102234212 63.0 19120 303.6
23:47:28.686 INFO ProgressMeter - chr7:116699730 63.2 19190 303.7
23:47:39.846 INFO ProgressMeter - chr7:116795885 63.4 19250 303.8
23:47:50.046 INFO ProgressMeter - chr7:140752633 63.5 19300 303.7
23:48:01.497 INFO ProgressMeter - chr7:140792543 63.7 19350 303.6
23:48:12.854 INFO ProgressMeter - chr7:140919195 63.9 19420 303.8
23:48:23.108 INFO ProgressMeter - chr7:152139184 64.1 19500 304.2
23:48:34.658 INFO ProgressMeter - chr7:152167253 64.3 19560 304.3
23:48:44.799 INFO ProgressMeter - chr7:152181209 64.5 19590 303.9
23:48:55.668 INFO ProgressMeter - chr7:152309964 64.6 19650 304.0
23:49:06.363 INFO ProgressMeter - chr8:26370215 64.8 19720 304.2
23:49:19.070 INFO ProgressMeter - chr8:32647400 65.0 19780 304.2
23:49:29.837 INFO ProgressMeter - chr8:32763987 65.2 19820 304.0
23:49:40.015 INFO ProgressMeter - chr8:37842092 65.4 19880 304.1
23:49:51.707 INFO ProgressMeter - chr8:41932203 65.6 19950 304.2
23:50:03.343 INFO ProgressMeter - chr8:41977181 65.8 20000 304.1
23:50:15.740 INFO ProgressMeter - chr8:47831812 66.0 20060 304.1
23:50:26.747 INFO ProgressMeter - chr8:47897178 66.2 20120 304.1
23:50:36.867 INFO ProgressMeter - chr8:54459407 66.3 20180 304.3
23:50:48.054 INFO ProgressMeter - chr8:68115751 66.5 20250 304.5
23:50:58.440 INFO ProgressMeter - chr8:91960505 66.7 20320 304.7
23:51:08.504 INFO ProgressMeter - chr8:127731443 66.9 20370 304.7
23:51:20.286 INFO ProgressMeter - chr8:127741989 67.0 20420 304.6
23:51:31.234 INFO ProgressMeter - chr8:144516124 67.2 20470 304.5
23:51:42.346 INFO ProgressMeter - chr9:5080620 67.4 20530 304.5
23:51:53.072 INFO ProgressMeter - chr9:8484117 67.6 20600 304.8
23:52:04.921 INFO ProgressMeter - chr9:20414062 67.8 20650 304.6
23:52:15.831 INFO ProgressMeter - chr9:35078613 68.0 20710 304.7
23:52:26.295 INFO ProgressMeter - chr9:83977766 68.1 20770 304.8
23:52:40.827 INFO ProgressMeter - chr9:84743519 68.4 20810 304.3
23:52:51.716 INFO ProgressMeter - chr9:84812447 68.6 20850 304.1
23:53:02.495 INFO ProgressMeter - chr9:84814338 68.8 20870 303.6
23:53:14.098 INFO ProgressMeter - chr9:84863039 68.9 20900 303.1
23:53:26.251 INFO ProgressMeter - chr9:84866166 69.1 20930 302.7
23:53:39.210 INFO ProgressMeter - chr9:84875166 69.4 20970 302.3
23:53:51.586 INFO ProgressMeter - chr9:85022655 69.6 21010 302.0
23:54:05.335 INFO ProgressMeter - chr9:90843951 69.8 21040 301.4
23:54:15.862 INFO ProgressMeter - chr9:95453476 70.0 21100 301.5
23:54:27.380 INFO ProgressMeter - chr9:99142534 70.2 21170 301.7
23:54:40.850 INFO ProgressMeter - chr9:130885118 70.4 21240 301.7
23:54:51.517 INFO ProgressMeter - chr9:132906729 70.6 21280 301.6
23:55:06.332 INFO ProgressMeter - chr9:136505637 70.8 21330 301.2
23:55:16.714 INFO ProgressMeter - chr9:136900420 71.0 21390 301.3
23:55:28.115 INFO ProgressMeter - chrX:40063615 71.2 21460 301.5
23:55:38.657 INFO ProgressMeter - chrX:45053827 71.4 21510 301.5
23:55:50.471 INFO ProgressMeter - chrX:47179317 71.6 21560 301.3
23:56:01.502 INFO ProgressMeter - chrX:48793791 71.7 21620 301.4
23:56:12.838 INFO ProgressMeter - chrX:49036207 71.9 21660 301.2
23:56:23.607 INFO ProgressMeter - chrX:53192819 72.1 21700 301.0
23:56:33.752 INFO ProgressMeter - chrX:53217794 72.3 21750 300.9
23:56:45.617 INFO ProgressMeter - chrX:53412257 72.5 21810 301.0
23:56:58.158 INFO ProgressMeter - chrX:64193250 72.7 21860 300.8
23:57:08.899 INFO ProgressMeter - chrX:67632654 72.9 21900 300.6
23:57:19.382 INFO ProgressMeter - chrX:71124322 73.0 21960 300.7
23:57:30.664 INFO ProgressMeter - chrX:71366313 73.2 22020 300.7
23:57:41.849 INFO ProgressMeter - chrX:77508412 73.4 22090 300.9
23:57:52.861 INFO ProgressMeter - chrX:77683189 73.6 22150 301.0
23:58:03.199 INFO ProgressMeter - chrX:111142170 73.8 22220 301.2
23:58:14.243 INFO ProgressMeter - chrX:124066354 73.9 22290 301.4
23:58:25.947 INFO ProgressMeter - chrX:130015586 74.1 22350 301.4
23:58:33.287 INFO Mutect2 - 744292 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
5 read(s) filtered by: ReadLengthReadFilter
165 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
744462 total reads filtered out of 110748454 reads processed
23:58:33.287 INFO ProgressMeter - chrY:21207343 74.3 22430 302.0
23:58:33.287 INFO ProgressMeter - Traversal complete. Processed 22430 total regions in 74.3 minutes.
23:58:33.302 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 9.181783808
23:58:33.303 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 373.47039928500004
23:58:33.303 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 13.71 sec
23:58:33.303 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:58:33 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 74.28 minutes.
Runtime.totalMemory()=3825205248
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 LS0901_tumor.bam --tumor-sample LS0901 -L TST500C_manifest.bed -O LS0901.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:58:34.906 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
23:58:35.018 INFO FilterMutectCalls - ------------------------------------------------------------
23:58:35.021 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:58:35.021 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:58:35.021 INFO FilterMutectCalls - Executing as ?@nf-d390ff9cd0838e558429d3a67b8380f9-4f610-d8n6j on Linux v6.12.88 amd64
23:58:35.021 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:58:35.021 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:58:34 PM GMT
23:58:35.021 INFO FilterMutectCalls - ------------------------------------------------------------
23:58:35.021 INFO FilterMutectCalls - ------------------------------------------------------------
23:58:35.022 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:58:35.022 INFO FilterMutectCalls - Picard Version: 3.1.1
23:58:35.022 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:58:35.022 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:58:35.022 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:58:35.022 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:58:35.022 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:58:35.023 INFO FilterMutectCalls - Deflater: IntelDeflater
23:58:35.023 INFO FilterMutectCalls - Inflater: IntelInflater
23:58:35.023 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:58:35.023 INFO FilterMutectCalls - Requester pays: disabled
23:58:35.023 INFO FilterMutectCalls - Initializing engine
23:58:35.197 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.jjWVPf1sjl/LS0901.mutect2.raw.vcf.gz
23:58:35.308 INFO FilterMutectCalls - Done initializing engine
23:58:35.363 INFO ProgressMeter - Starting traversal
23:58:35.364 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:58:35.364 INFO FilterMutectCalls - Starting pass 0 through the variants
23:58:36.843 INFO FilterMutectCalls - Finished pass 0 through the variants
23:58:39.764 INFO FilterMutectCalls - Starting pass 1 through the variants
23:58:41.714 INFO FilterMutectCalls - Finished pass 1 through the variants
23:58:42.325 INFO FilterMutectCalls - Starting pass 2 through the variants
23:58:44.255 INFO FilterMutectCalls - Finished pass 2 through the variants
23:58:44.256 INFO FilterMutectCalls - Starting pass 3 through the variants
23:58:45.646 INFO ProgressMeter - chr7:13973644 0.2 11000 64208.6
23:58:45.927 INFO FilterMutectCalls - Finished pass 3 through the variants
23:58:45.933 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
23:58:45.934 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
23:58:45.934 INFO ProgressMeter - chr7:13973644 0.2 11520 65392.6
23:58:45.934 INFO ProgressMeter - Traversal complete. Processed 11520 total variants in 0.2 minutes.
23:58:45.944 INFO FilterMutectCalls - Shutting down engine
[June 8, 2026 at 11:58:45 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=327155712
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 LS0901.mutect2.raw.vcf.gz --stats LS0901.mutect2.raw.vcf.gz.stats -O LS0901.mutect2.filtered.vcf.gz
23:58:47.139 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
23:58:47.258 INFO SelectVariants - ------------------------------------------------------------
23:58:47.260 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:58:47.261 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
23:58:47.261 INFO SelectVariants - Executing as ?@nf-d390ff9cd0838e558429d3a67b8380f9-4f610-d8n6j on Linux v6.12.88 amd64
23:58:47.261 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:58:47.261 INFO SelectVariants - Start Date/Time: June 8, 2026 at 11:58:47 PM GMT
23:58:47.261 INFO SelectVariants - ------------------------------------------------------------
23:58:47.261 INFO SelectVariants - ------------------------------------------------------------
23:58:47.262 INFO SelectVariants - HTSJDK Version: 4.1.0
23:58:47.262 INFO SelectVariants - Picard Version: 3.1.1
23:58:47.262 INFO SelectVariants - Built for Spark Version: 3.5.0
23:58:47.262 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:58:47.263 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:58:47.263 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:58:47.263 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:58:47.263 INFO SelectVariants - Deflater: IntelDeflater
23:58:47.263 INFO SelectVariants - Inflater: IntelInflater
23:58:47.263 INFO SelectVariants - GCS max retries/reopens: 20
23:58:47.263 INFO SelectVariants - Requester pays: disabled
23:58:47.263 INFO SelectVariants - Initializing engine
23:58:47.454 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.jjWVPf1sjl/LS0901.mutect2.filtered.vcf.gz
23:58:47.557 INFO SelectVariants - Done initializing engine
23:58:47.592 INFO ProgressMeter - Starting traversal
23:58:47.593 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:58:47.667 INFO ProgressMeter - chr5:177099907 0.0 2880 2400000.0
23:58:47.667 INFO ProgressMeter - Traversal complete. Processed 2880 total variants in 0.0 minutes.
23:58:47.678 INFO SelectVariants - Shutting down engine
[June 8, 2026 at 11:58:47 PM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=486539264
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 LS0901.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0901.mutect2.pass.vcf.gz