22:44:33.873 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
22:44:33.963 INFO Mutect2 - ------------------------------------------------------------
22:44:33.965 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:33.966 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:33.966 INFO Mutect2 - Executing as ?@nf-02794f7555b116425cfe88a12543c0a2-7af98-jpw64 on Linux v6.12.88 amd64
22:44:33.966 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:33.966 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:33 PM GMT
22:44:33.966 INFO Mutect2 - ------------------------------------------------------------
22:44:33.966 INFO Mutect2 - ------------------------------------------------------------
22:44:33.967 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:33.967 INFO Mutect2 - Picard Version: 3.1.1
22:44:33.967 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:33.967 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:33.967 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:33.967 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:33.967 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:33.967 INFO Mutect2 - Deflater: IntelDeflater
22:44:33.967 INFO Mutect2 - Inflater: IntelInflater
22:44:33.967 INFO Mutect2 - GCS max retries/reopens: 20
22:44:33.968 INFO Mutect2 - Requester pays: disabled
22:44:33.968 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.WHLt03qVLO/LS0917_tumor.bam.bai is older than BAM /tmp/nxf.WHLt03qVLO/LS0917_tumor.bam
22:44:34.117 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.WHLt03qVLO/af-only-gnomad.hg38.vcf.gz
22:44:34.250 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.WHLt03qVLO/TST500C_manifest.bed
22:44:34.284 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:34.313 INFO Mutect2 - Done initializing engine
22:44:34.322 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
22:44:34.324 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
22:44:34.324 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:34.325 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:34.333 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
22:44:34.341 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:34.341 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:34.342 INFO IntelPairHmm - Available threads: 384
22:44:34.342 INFO IntelPairHmm - Requested threads: 4
22:44:34.342 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:34.376 INFO ProgressMeter - Starting traversal
22:44:34.376 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:44.427 INFO ProgressMeter - chr1:8014318 0.2 30 179.1
22:44:56.022 INFO ProgressMeter - chr1:11126620 0.4 90 249.5
22:45:10.136 INFO ProgressMeter - chr1:11234141 0.6 150 251.7
22:45:23.486 INFO ProgressMeter - chr1:15928748 0.8 200 244.3
22:45:36.626 INFO ProgressMeter - chr1:15933043 1.0 240 231.3
22:45:47.354 INFO ProgressMeter - chr1:15939389 1.2 280 230.2
22:45:58.673 INFO ProgressMeter - chr1:18745928 1.4 330 234.9
22:46:09.296 INFO ProgressMeter - chr1:23559125 1.6 360 227.6
22:46:19.978 INFO ProgressMeter - chr1:26774736 1.8 410 233.0
22:46:30.900 INFO ProgressMeter - chr1:36468109 1.9 460 236.9
22:46:41.691 INFO ProgressMeter - chr1:39898401 2.1 510 240.3
22:46:53.322 INFO ProgressMeter - chr1:43339962 2.3 560 241.8
22:47:05.071 INFO ProgressMeter - chr1:46066052 2.5 620 246.9
22:47:16.057 INFO ProgressMeter - chr1:58782187 2.7 680 252.3
22:47:27.270 INFO ProgressMeter - chr1:64883412 2.9 740 256.8
22:47:38.052 INFO ProgressMeter - chr1:114706462 3.1 800 261.3
22:47:48.920 INFO ProgressMeter - chr1:117623050 3.2 870 268.3
22:47:59.728 INFO ProgressMeter - chr1:119916151 3.4 900 263.0
22:48:10.286 INFO ProgressMeter - chr1:119948464 3.6 940 261.2
22:48:22.294 INFO ProgressMeter - chr1:156871789 3.8 1000 263.3
22:48:32.929 INFO ProgressMeter - chr1:156872853 4.0 1010 254.0
22:48:51.714 INFO ProgressMeter - chr1:156879120 4.3 1040 242.5
22:49:02.231 INFO ProgressMeter - chr1:158645201 4.5 1090 244.2
22:49:13.736 INFO ProgressMeter - chr1:160816910 4.7 1150 247.0
22:49:23.836 INFO ProgressMeter - chr1:175989360 4.8 1200 248.7
22:49:35.221 INFO ProgressMeter - chr1:179121844 5.0 1250 249.3
22:49:47.578 INFO ProgressMeter - chr1:204444329 5.2 1320 252.9
22:49:57.624 INFO ProgressMeter - chr1:204521148 5.4 1360 252.4
22:50:09.858 INFO ProgressMeter - chr1:204556136 5.6 1410 252.2
22:50:20.488 INFO ProgressMeter - chr1:226367499 5.8 1470 254.8
22:50:32.676 INFO ProgressMeter - chr1:241508601 6.0 1530 256.2
22:50:45.782 INFO ProgressMeter - chr1:243502710 6.2 1570 253.6
22:50:57.067 INFO ProgressMeter - chr1:243552918 6.4 1600 250.9
22:51:07.696 INFO ProgressMeter - chr10:27029265 6.6 1650 251.7
22:51:19.011 INFO ProgressMeter - chr10:27077417 6.7 1700 252.1
22:51:30.589 INFO ProgressMeter - chr10:32018152 6.9 1740 250.8
22:51:41.019 INFO ProgressMeter - chr10:43106702 7.1 1800 253.1
22:51:54.672 INFO ProgressMeter - chr10:43114709 7.3 1840 250.7
22:52:08.622 INFO ProgressMeter - chr10:43118037 7.6 1880 248.3
22:52:18.937 INFO ProgressMeter - chr10:62049478 7.7 1920 248.0
22:52:31.841 INFO ProgressMeter - chr10:68573815 8.0 1960 246.3
22:52:43.188 INFO ProgressMeter - chr10:68686701 8.1 2000 245.5
22:52:54.282 INFO ProgressMeter - chr10:87928751 8.3 2060 247.2
22:53:05.342 INFO ProgressMeter - chr10:101770361 8.5 2110 247.8
22:53:15.614 INFO ProgressMeter - chr10:102597138 8.7 2170 249.8
22:53:28.607 INFO ProgressMeter - chr10:110601001 8.9 2230 250.5
22:53:41.403 INFO ProgressMeter - chr10:121480583 9.1 2290 251.2
22:53:51.976 INFO ProgressMeter - chr10:121483029 9.3 2310 248.6
22:54:02.981 INFO ProgressMeter - chr10:121560711 9.5 2360 249.0
22:54:13.463 INFO ProgressMeter - chr11:17725454 9.7 2420 250.7
22:54:24.372 INFO ProgressMeter - chr11:64370561 9.8 2490 253.2
22:54:34.941 INFO ProgressMeter - chr11:69646181 10.0 2560 255.8
22:54:47.349 INFO ProgressMeter - chr11:69700020 10.2 2620 256.5
22:54:57.458 INFO ProgressMeter - chr11:69768328 10.4 2660 256.1
22:55:08.656 INFO ProgressMeter - chr11:69778588 10.6 2710 256.4
22:55:18.695 INFO ProgressMeter - chr11:69810613 10.7 2730 254.2
22:55:29.804 INFO ProgressMeter - chr11:76472683 10.9 2780 254.5
22:55:42.107 INFO ProgressMeter - chr11:77349182 11.1 2830 254.3
22:55:52.159 INFO ProgressMeter - chr11:77422770 11.3 2880 254.9
22:56:02.402 INFO ProgressMeter - chr11:94490831 11.5 2950 257.3
22:56:13.145 INFO ProgressMeter - chr11:102162454 11.6 2990 256.7
22:56:24.588 INFO ProgressMeter - chr11:102325076 11.8 3010 254.3
22:56:34.932 INFO ProgressMeter - chr11:108282708 12.0 3070 255.6
22:56:45.034 INFO ProgressMeter - chr11:112093099 12.2 3140 257.8
22:56:56.711 INFO ProgressMeter - chr11:118481985 12.4 3190 257.8
22:57:09.303 INFO ProgressMeter - chr11:118504326 12.6 3240 257.5
22:57:19.558 INFO ProgressMeter - chr11:119232637 12.8 3280 257.2
22:57:32.336 INFO ProgressMeter - chr11:125629389 13.0 3320 256.1
22:57:43.899 INFO ProgressMeter - chr11:128458759 13.2 3370 256.1
22:57:56.950 INFO ProgressMeter - chr11:128462077 13.4 3400 254.2
22:58:07.712 INFO ProgressMeter - chr11:128810500 13.6 3450 254.5
22:58:17.856 INFO ProgressMeter - chr12:292877 13.7 3480 253.6
22:58:29.015 INFO ProgressMeter - chr12:914429 13.9 3540 254.5
22:58:39.119 INFO ProgressMeter - chr12:4373398 14.1 3590 255.0
22:58:51.212 INFO ProgressMeter - chr12:4436122 14.3 3640 254.9
22:59:01.810 INFO ProgressMeter - chr12:4445223 14.5 3670 253.9
22:59:13.135 INFO ProgressMeter - chr12:6593414 14.6 3730 254.7
22:59:26.042 INFO ProgressMeter - chr12:11853668 14.9 3770 253.7
22:59:37.989 INFO ProgressMeter - chr12:11857469 15.1 3800 252.3
22:59:48.747 INFO ProgressMeter - chr12:11861153 15.2 3830 251.3
23:00:01.122 INFO ProgressMeter - chr12:11864486 15.4 3870 250.6
23:00:11.307 INFO ProgressMeter - chr12:11866604 15.6 3890 249.1
23:00:26.661 INFO ProgressMeter - chr12:11869527 15.9 3920 247.0
23:00:36.794 INFO ProgressMeter - chr12:18497627 16.0 3980 248.1
23:00:47.062 INFO ProgressMeter - chr12:25224192 16.2 4030 248.6
23:00:57.279 INFO ProgressMeter - chr12:45836600 16.4 4080 249.1
23:01:08.450 INFO ProgressMeter - chr12:45852607 16.6 4120 248.7
23:01:22.133 INFO ProgressMeter - chr12:49032379 16.8 4180 248.9
23:01:34.966 INFO ProgressMeter - chr12:49038261 17.0 4210 247.5
23:01:45.824 INFO ProgressMeter - chr12:49046698 17.2 4260 247.8
23:01:56.080 INFO ProgressMeter - chr12:49053976 17.4 4300 247.7
23:02:06.112 INFO ProgressMeter - chr12:56083316 17.5 4360 248.7
23:02:17.398 INFO ProgressMeter - chr12:56101245 17.7 4420 249.5
23:02:28.638 INFO ProgressMeter - chr12:57094438 17.9 4460 249.1
23:02:39.212 INFO ProgressMeter - chr12:57743926 18.1 4510 249.4
23:02:49.298 INFO ProgressMeter - chr12:68816810 18.2 4570 250.4
23:02:59.942 INFO ProgressMeter - chr12:69570490 18.4 4630 251.3
23:03:11.088 INFO ProgressMeter - chr12:112482072 18.6 4690 252.0
23:03:22.372 INFO ProgressMeter - chr12:120994172 18.8 4740 252.1
23:03:33.645 INFO ProgressMeter - chr12:132643970 19.0 4790 252.3
23:03:44.121 INFO ProgressMeter - chr12:132681136 19.2 4850 253.1
23:03:54.564 INFO ProgressMeter - chr13:21671983 19.3 4890 252.9
23:04:04.741 INFO ProgressMeter - chr13:21700126 19.5 4940 253.3
23:04:16.552 INFO ProgressMeter - chr13:28050107 19.7 5010 254.3
23:04:27.704 INFO ProgressMeter - chr13:28384992 19.9 5060 254.4
23:04:41.081 INFO ProgressMeter - chr13:28388872 20.1 5090 253.1
23:04:53.173 INFO ProgressMeter - chr13:32332630 20.3 5140 253.0
23:05:05.510 INFO ProgressMeter - chr13:32339378 20.5 5180 252.5
23:05:15.648 INFO ProgressMeter - chr13:32370460 20.7 5220 252.3
23:05:26.270 INFO ProgressMeter - chr13:48347823 20.9 5270 252.6
23:05:37.854 INFO ProgressMeter - chr13:101726789 21.1 5340 253.6
23:05:48.757 INFO ProgressMeter - chr13:102852130 21.2 5400 254.2
23:05:59.399 INFO ProgressMeter - chr13:109767154 21.4 5450 254.5
23:06:10.926 INFO ProgressMeter - chr13:113308034 21.6 5510 255.0
23:06:22.470 INFO ProgressMeter - chr14:23308814 21.8 5550 254.6
23:06:33.751 INFO ProgressMeter - chr14:37591149 22.0 5610 255.1
23:06:45.152 INFO ProgressMeter - chr14:37598403 22.2 5660 255.2
23:06:55.596 INFO ProgressMeter - chr14:80955679 22.4 5720 255.9
23:07:05.666 INFO ProgressMeter - chr14:95096399 22.5 5760 255.8
23:07:16.015 INFO ProgressMeter - chr14:102082168 22.7 5810 256.0
23:07:27.879 INFO ProgressMeter - chr15:32734498 22.9 5870 256.4
23:07:38.849 INFO ProgressMeter - chr15:34354539 23.1 5900 255.7
23:07:50.276 INFO ProgressMeter - chr15:41668893 23.3 5950 255.7
23:08:02.666 INFO ProgressMeter - chr15:41739904 23.5 5990 255.2
23:08:13.246 INFO ProgressMeter - chr15:41764884 23.6 6030 255.0
23:08:23.992 INFO ProgressMeter - chr15:49447484 23.8 6080 255.2
23:08:34.718 INFO ProgressMeter - chr15:73699638 24.0 6140 255.8
23:08:47.026 INFO ProgressMeter - chr15:87978934 24.2 6190 255.7
23:08:58.120 INFO ProgressMeter - chr15:89285179 24.4 6250 256.2
23:09:09.701 INFO ProgressMeter - chr15:90760145 24.6 6310 256.6
23:09:20.212 INFO ProgressMeter - chr15:92939611 24.8 6360 256.8
23:09:30.743 INFO ProgressMeter - chr15:93014792 24.9 6420 257.4
23:09:42.355 INFO ProgressMeter - chr15:98957339 25.1 6470 257.4
23:09:53.634 INFO ProgressMeter - chr16:2074261 25.3 6530 257.9
23:10:03.837 INFO ProgressMeter - chr16:2175109 25.5 6590 258.5
23:10:13.910 INFO ProgressMeter - chr16:3591027 25.7 6650 259.2
23:10:26.443 INFO ProgressMeter - chr16:3729089 25.9 6690 258.6
23:10:39.052 INFO ProgressMeter - chr16:9763387 26.1 6760 259.2
23:10:50.675 INFO ProgressMeter - chr16:9938326 26.3 6800 258.8
23:11:02.364 INFO ProgressMeter - chr16:23629947 26.5 6860 259.2
23:11:12.844 INFO ProgressMeter - chr16:50749697 26.6 6910 259.4
23:11:24.027 INFO ProgressMeter - chr16:56838968 26.8 6970 259.8
23:11:36.013 INFO ProgressMeter - chr16:68829652 27.0 7030 260.1
23:11:47.376 INFO ProgressMeter - chr16:72794812 27.2 7060 259.4
23:11:59.670 INFO ProgressMeter - chr16:72798177 27.4 7090 258.6
23:12:11.988 INFO ProgressMeter - chr16:72959684 27.6 7130 258.1
23:12:23.521 INFO ProgressMeter - chr16:81956693 27.8 7190 258.5
23:12:36.014 INFO ProgressMeter - chr16:89283352 28.0 7240 258.3
23:12:46.906 INFO ProgressMeter - chr16:89290623 28.2 7270 257.7
23:12:57.550 INFO ProgressMeter - chr16:89808292 28.4 7340 258.6
23:13:09.155 INFO ProgressMeter - chr17:7674899 28.6 7400 258.9
23:13:20.664 INFO ProgressMeter - chr17:7682667 28.8 7430 258.2
23:13:32.108 INFO ProgressMeter - chr17:16040439 29.0 7500 259.0
23:13:44.431 INFO ProgressMeter - chr17:16101688 29.2 7550 258.8
23:13:56.698 INFO ProgressMeter - chr17:18039463 29.4 7620 259.4
23:14:08.585 INFO ProgressMeter - chr17:31235916 29.6 7680 259.7
23:14:18.688 INFO ProgressMeter - chr17:31374011 29.7 7730 259.9
23:14:29.251 INFO ProgressMeter - chr17:39470975 29.9 7790 260.4
23:14:39.786 INFO ProgressMeter - chr17:39700068 30.1 7840 260.6
23:14:50.092 INFO ProgressMeter - chr17:39725325 30.3 7890 260.7
23:15:00.536 INFO ProgressMeter - chr17:40401074 30.4 7950 261.2
23:15:10.628 INFO ProgressMeter - chr17:42227527 30.6 8010 261.7
23:15:21.066 INFO ProgressMeter - chr17:43049325 30.8 8080 262.5
23:15:33.687 INFO ProgressMeter - chr17:43091865 31.0 8130 262.4
23:15:44.055 INFO ProgressMeter - chr17:43094075 31.2 8150 261.5
23:15:54.575 INFO ProgressMeter - chr17:43529133 31.3 8190 261.4
23:16:05.226 INFO ProgressMeter - chr17:43533920 31.5 8220 260.8
23:16:16.524 INFO ProgressMeter - chr17:43536940 31.7 8240 259.9
23:16:28.845 INFO ProgressMeter - chr17:43541236 31.9 8280 259.5
23:16:40.990 INFO ProgressMeter - chr17:43543347 32.1 8300 258.5
23:16:52.659 INFO ProgressMeter - chr17:45274187 32.3 8340 258.2
23:17:04.776 INFO ProgressMeter - chr17:58357868 32.5 8390 258.1
23:17:15.004 INFO ProgressMeter - chr17:59899825 32.7 8440 258.3
23:17:25.779 INFO ProgressMeter - chr17:59947416 32.9 8500 258.7
23:17:37.745 INFO ProgressMeter - chr17:61808658 33.1 8550 258.7
23:17:48.521 INFO ProgressMeter - chr17:65537746 33.2 8600 258.8
23:17:59.663 INFO ProgressMeter - chr17:72126258 33.4 8650 258.8
23:18:11.411 INFO ProgressMeter - chr17:80957622 33.6 8710 259.1
23:18:22.144 INFO ProgressMeter - chr18:41987810 33.8 8770 259.5
23:18:33.666 INFO ProgressMeter - chr18:44951541 34.0 8820 259.5
23:18:44.230 INFO ProgressMeter - chr18:47870473 34.2 8860 259.3
23:18:55.118 INFO ProgressMeter - chr18:59904512 34.3 8920 259.7
23:19:06.207 INFO ProgressMeter - chr19:2193687 34.5 8990 260.3
23:19:16.585 INFO ProgressMeter - chr19:4047734 34.7 9050 260.8
23:19:27.132 INFO ProgressMeter - chr19:5215322 34.9 9110 261.2
23:19:38.206 INFO ProgressMeter - chr19:7125345 35.1 9170 261.5
23:19:49.421 INFO ProgressMeter - chr19:10143764 35.3 9230 261.8
23:19:59.950 INFO ProgressMeter - chr19:10489213 35.4 9280 262.0
23:20:10.878 INFO ProgressMeter - chr19:11027782 35.6 9340 262.3
23:20:21.510 INFO ProgressMeter - chr19:14516789 35.8 9390 262.4
23:20:32.482 INFO ProgressMeter - chr19:15179235 36.0 9440 262.5
23:20:42.514 INFO ProgressMeter - chr19:15197549 36.1 9480 262.3
23:20:53.039 INFO ProgressMeter - chr19:15273020 36.3 9530 262.5
23:21:03.925 INFO ProgressMeter - chr19:18167187 36.5 9590 262.8
23:21:14.919 INFO ProgressMeter - chr19:29817404 36.7 9640 262.8
23:21:27.203 INFO ProgressMeter - chr19:35720904 36.9 9700 263.0
23:21:38.892 INFO ProgressMeter - chr19:35733432 37.1 9760 263.2
23:21:50.313 INFO ProgressMeter - chr19:40270464 37.3 9820 263.5
23:22:06.591 INFO ProgressMeter - chr19:41260381 37.5 9880 263.2
23:22:16.761 INFO ProgressMeter - chr19:42291187 37.7 9930 263.4
23:22:27.424 INFO ProgressMeter - chr19:45357830 37.9 9980 263.4
23:22:37.462 INFO ProgressMeter - chr19:45409331 38.1 10040 263.9
23:22:48.347 INFO ProgressMeter - chr19:50398856 38.2 10100 264.2
23:22:58.922 INFO ProgressMeter - chr19:52221075 38.4 10170 264.8
23:23:10.732 INFO ProgressMeter - chr2:15943386 38.6 10210 264.5
23:23:21.418 INFO ProgressMeter - chr2:17780805 38.8 10260 264.5
23:23:34.351 INFO ProgressMeter - chr2:25282512 39.0 10310 264.4
23:23:45.135 INFO ProgressMeter - chr2:25749994 39.2 10340 263.9
23:23:57.704 INFO ProgressMeter - chr2:29222787 39.4 10390 263.8
23:24:12.509 INFO ProgressMeter - chr2:29226370 39.6 10420 262.9
23:24:23.800 INFO ProgressMeter - chr2:29911828 39.8 10470 262.9
23:24:33.854 INFO ProgressMeter - chr2:42303313 40.0 10510 262.8
23:24:44.857 INFO ProgressMeter - chr2:47379767 40.2 10550 262.6
23:24:56.292 INFO ProgressMeter - chr2:47478326 40.4 10580 262.1
23:25:06.733 INFO ProgressMeter - chr2:47801104 40.5 10620 262.0
23:25:17.502 INFO ProgressMeter - chr2:61492103 40.7 10690 262.5
23:25:27.699 INFO ProgressMeter - chr2:98543875 40.9 10740 262.7
23:25:39.033 INFO ProgressMeter - chr2:108763398 41.1 10810 263.2
23:25:50.023 INFO ProgressMeter - chr2:108772970 41.3 10860 263.2
23:26:06.506 INFO ProgressMeter - chr2:111127650 41.5 10900 262.4
23:26:17.680 INFO ProgressMeter - chr2:113221030 41.7 10930 262.0
23:26:27.782 INFO ProgressMeter - chr2:113223968 41.9 10960 261.6
23:26:38.731 INFO ProgressMeter - chr2:113226084 42.1 10980 261.0
23:26:53.576 INFO ProgressMeter - chr2:113229613 42.3 11010 260.2
23:27:13.464 INFO ProgressMeter - chr2:113232931 42.7 11050 259.1
23:27:24.073 INFO ProgressMeter - chr2:113235064 42.8 11070 258.5
23:27:34.383 INFO ProgressMeter - chr2:136112431 43.0 11130 258.8
23:27:44.736 INFO ProgressMeter - chr2:140444380 43.2 11190 259.2
23:27:56.218 INFO ProgressMeter - chr2:140850100 43.4 11250 259.4
23:28:07.766 INFO ProgressMeter - chr2:141229181 43.6 11300 259.4
23:28:20.220 INFO ProgressMeter - chr2:168943744 43.8 11330 258.9
23:28:31.993 INFO ProgressMeter - chr2:189864022 44.0 11390 259.1
23:28:43.639 INFO ProgressMeter - chr2:197407996 44.2 11460 259.5
23:28:54.707 INFO ProgressMeter - chr2:208245317 44.3 11520 259.8
23:29:05.100 INFO ProgressMeter - chr2:214730409 44.5 11580 260.2
23:29:17.144 INFO ProgressMeter - chr2:222200951 44.7 11630 260.1
23:29:27.963 INFO ProgressMeter - chr2:222203110 44.9 11650 259.5
23:29:40.220 INFO ProgressMeter - chr2:222206357 45.1 11680 259.0
23:29:54.367 INFO ProgressMeter - chr2:222210791 45.3 11720 258.5
23:30:04.471 INFO ProgressMeter - chr2:222213621 45.5 11750 258.2
23:30:18.513 INFO ProgressMeter - chr2:222217183 45.7 11780 257.6
23:30:29.395 INFO ProgressMeter - chr2:222220400 45.9 11810 257.2
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00:15:26.598 INFO Mutect2 - 937551 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
7 read(s) filtered by: ReadLengthReadFilter
167 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
937725 total reads filtered out of 153631840 reads processed
00:15:26.598 INFO ProgressMeter - chrY:20489365 90.9 22374 246.2
00:15:26.598 INFO ProgressMeter - Traversal complete. Processed 22374 total regions in 90.9 minutes.
00:15:26.613 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 10.032279604000001
00:15:26.613 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 466.633851158
00:15:26.613 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 17.34 sec
00:15:26.614 INFO Mutect2 - Shutting down engine
[June 9, 2026 at 12:15:26 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 90.88 minutes.
Runtime.totalMemory()=5628755968
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 LS0917_tumor.bam --tumor-sample LS0917 -L TST500C_manifest.bed -O LS0917.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
00:15:28.328 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
00:15:28.426 INFO FilterMutectCalls - ------------------------------------------------------------
00:15:28.428 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
00:15:28.428 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
00:15:28.428 INFO FilterMutectCalls - Executing as ?@nf-02794f7555b116425cfe88a12543c0a2-7af98-jpw64 on Linux v6.12.88 amd64
00:15:28.428 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
00:15:28.429 INFO FilterMutectCalls - Start Date/Time: June 9, 2026 at 12:15:28 AM GMT
00:15:28.429 INFO FilterMutectCalls - ------------------------------------------------------------
00:15:28.429 INFO FilterMutectCalls - ------------------------------------------------------------
00:15:28.430 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
00:15:28.430 INFO FilterMutectCalls - Picard Version: 3.1.1
00:15:28.430 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
00:15:28.430 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:15:28.430 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:15:28.430 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:15:28.431 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:15:28.431 INFO FilterMutectCalls - Deflater: IntelDeflater
00:15:28.431 INFO FilterMutectCalls - Inflater: IntelInflater
00:15:28.431 INFO FilterMutectCalls - GCS max retries/reopens: 20
00:15:28.431 INFO FilterMutectCalls - Requester pays: disabled
00:15:28.431 INFO FilterMutectCalls - Initializing engine
00:15:28.592 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.WHLt03qVLO/LS0917.mutect2.raw.vcf.gz
00:15:28.701 INFO FilterMutectCalls - Done initializing engine
00:15:28.752 INFO ProgressMeter - Starting traversal
00:15:28.753 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
00:15:28.753 INFO FilterMutectCalls - Starting pass 0 through the variants
00:15:30.442 INFO FilterMutectCalls - Finished pass 0 through the variants
00:15:33.151 INFO FilterMutectCalls - Starting pass 1 through the variants
00:15:35.029 INFO FilterMutectCalls - Finished pass 1 through the variants
00:15:35.710 INFO FilterMutectCalls - Starting pass 2 through the variants
00:15:37.556 INFO FilterMutectCalls - Finished pass 2 through the variants
00:15:37.558 INFO FilterMutectCalls - Starting pass 3 through the variants
00:15:39.079 INFO FilterMutectCalls - Finished pass 3 through the variants
00:15:39.085 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
00:15:39.086 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
00:15:39.086 INFO ProgressMeter - chr4:105275794 0.2 10976 63733.7
00:15:39.086 INFO ProgressMeter - Traversal complete. Processed 10976 total variants in 0.2 minutes.
00:15:39.097 INFO FilterMutectCalls - Shutting down engine
[June 9, 2026 at 12:15:39 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=226492416
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 LS0917.mutect2.raw.vcf.gz --stats LS0917.mutect2.raw.vcf.gz.stats -O LS0917.mutect2.filtered.vcf.gz
00:15:40.188 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
00:15:40.274 INFO SelectVariants - ------------------------------------------------------------
00:15:40.276 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
00:15:40.276 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
00:15:40.276 INFO SelectVariants - Executing as ?@nf-02794f7555b116425cfe88a12543c0a2-7af98-jpw64 on Linux v6.12.88 amd64
00:15:40.277 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
00:15:40.277 INFO SelectVariants - Start Date/Time: June 9, 2026 at 12:15:40 AM GMT
00:15:40.277 INFO SelectVariants - ------------------------------------------------------------
00:15:40.277 INFO SelectVariants - ------------------------------------------------------------
00:15:40.277 INFO SelectVariants - HTSJDK Version: 4.1.0
00:15:40.277 INFO SelectVariants - Picard Version: 3.1.1
00:15:40.277 INFO SelectVariants - Built for Spark Version: 3.5.0
00:15:40.278 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:15:40.278 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:15:40.278 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:15:40.278 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:15:40.278 INFO SelectVariants - Deflater: IntelDeflater
00:15:40.278 INFO SelectVariants - Inflater: IntelInflater
00:15:40.278 INFO SelectVariants - GCS max retries/reopens: 20
00:15:40.278 INFO SelectVariants - Requester pays: disabled
00:15:40.278 INFO SelectVariants - Initializing engine
00:15:40.392 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.WHLt03qVLO/LS0917.mutect2.filtered.vcf.gz
00:15:40.484 INFO SelectVariants - Done initializing engine
00:15:40.517 INFO ProgressMeter - Starting traversal
00:15:40.517 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
00:15:40.587 INFO ProgressMeter - chr6:36677919 0.0 2744 2421176.5
00:15:40.587 INFO ProgressMeter - Traversal complete. Processed 2744 total variants in 0.0 minutes.
00:15:40.597 INFO SelectVariants - Shutting down engine
[June 9, 2026 at 12:15:40 AM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=503316480
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 LS0917.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0917.mutect2.pass.vcf.gz