Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/bb/f9165f87084e3e9d333c2b1e913cfb/.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/bb/f9165f87084e3e9d333c2b1e913cfb/.command.run
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0880/LS0880_tumor.bam
Downloading: s3://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0880/LS0880_tumor.bam.bai
==> STAGING COMPLETE (10 inputs)
22:44:26.119 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
22:44:26.234 INFO Mutect2 - ------------------------------------------------------------
22:44:26.237 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
22:44:26.237 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
22:44:26.237 INFO Mutect2 - Executing as ?@nf-bbf9165f87084e3e9d333c2b1e913cfb-5a867-v46zv on Linux v6.12.88 amd64
22:44:26.237 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
22:44:26.237 INFO Mutect2 - Start Date/Time: June 8, 2026 at 10:44:26 PM GMT
22:44:26.237 INFO Mutect2 - ------------------------------------------------------------
22:44:26.237 INFO Mutect2 - ------------------------------------------------------------
22:44:26.239 INFO Mutect2 - HTSJDK Version: 4.1.0
22:44:26.239 INFO Mutect2 - Picard Version: 3.1.1
22:44:26.239 INFO Mutect2 - Built for Spark Version: 3.5.0
22:44:26.239 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:44:26.239 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:44:26.239 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:44:26.240 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:44:26.240 INFO Mutect2 - Deflater: IntelDeflater
22:44:26.240 INFO Mutect2 - Inflater: IntelInflater
22:44:26.241 INFO Mutect2 - GCS max retries/reopens: 20
22:44:26.241 INFO Mutect2 - Requester pays: disabled
22:44:26.241 INFO Mutect2 - Initializing engine
WARNING: BAM index file /tmp/nxf.4jR2jrxr2i/LS0880_tumor.bam.bai is older than BAM /tmp/nxf.4jR2jrxr2i/LS0880_tumor.bam
22:44:26.407 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.4jR2jrxr2i/af-only-gnomad.hg38.vcf.gz
22:44:26.537 INFO FeatureManager - Using codec BEDCodec to read file file:///tmp/nxf.4jR2jrxr2i/TST500C_manifest.bed
22:44:26.573 INFO IntervalArgumentCollection - Processing 1970331 bp from intervals
22:44:26.601 INFO Mutect2 - Done initializing engine
22:44:26.612 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
22:44:26.613 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
22:44:26.614 INFO IntelSmithWaterman - Using CPU-supported AVX-512 instructions
22:44:26.614 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:44:26.626 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
22:44:26.635 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
22:44:26.635 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:44:26.636 INFO IntelPairHmm - Available threads: 384
22:44:26.636 INFO IntelPairHmm - Requested threads: 4
22:44:26.636 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:44:26.685 INFO ProgressMeter - Starting traversal
22:44:26.686 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:44:37.981 INFO ProgressMeter - chr1:9716438 0.2 40 212.5
22:44:49.106 INFO ProgressMeter - chr1:11150124 0.4 100 267.6
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22:45:11.476 INFO ProgressMeter - chr1:15930973 0.7 190 254.5
22:45:24.168 INFO ProgressMeter - chr1:15937465 1.0 230 240.1
22:45:36.191 INFO ProgressMeter - chr1:18746059 1.2 280 241.7
22:45:46.643 INFO ProgressMeter - chr1:26696718 1.3 320 240.1
22:45:59.737 INFO ProgressMeter - chr1:26780224 1.6 370 238.6
22:46:11.300 INFO ProgressMeter - chr1:39894154 1.7 430 246.6
22:46:22.230 INFO ProgressMeter - chr1:39904253 1.9 480 249.3
22:46:33.215 INFO ProgressMeter - chr1:46046549 2.1 540 256.1
22:46:45.007 INFO ProgressMeter - chr1:64835394 2.3 610 264.6
22:46:55.482 INFO ProgressMeter - chr1:77960342 2.5 670 270.2
22:47:07.258 INFO ProgressMeter - chr1:117156699 2.7 750 280.2
22:47:19.979 INFO ProgressMeter - chr1:119916404 2.9 800 277.0
22:47:31.301 INFO ProgressMeter - chr1:119969573 3.1 850 276.3
22:47:43.737 INFO ProgressMeter - chr1:156873188 3.3 900 274.0
22:47:54.623 INFO ProgressMeter - chr1:156881569 3.5 930 268.4
22:48:04.971 INFO ProgressMeter - chr1:158656562 3.6 980 269.4
22:48:16.846 INFO ProgressMeter - chr1:162773467 3.8 1040 271.1
22:48:27.863 INFO ProgressMeter - chr1:179126375 4.0 1100 273.7
22:48:38.844 INFO ProgressMeter - chr1:204459876 4.2 1170 278.4
22:48:49.631 INFO ProgressMeter - chr1:204549111 4.4 1230 280.7
22:48:59.769 INFO ProgressMeter - chr1:206771354 4.6 1280 281.2
22:49:10.747 INFO ProgressMeter - chr1:241500435 4.7 1340 283.0
22:49:20.774 INFO ProgressMeter - chr1:243502185 4.9 1370 279.5
22:49:32.383 INFO ProgressMeter - chr1:243615094 5.1 1400 274.8
22:49:43.881 INFO ProgressMeter - chr10:27035025 5.3 1450 274.3
22:49:54.027 INFO ProgressMeter - chr10:27100064 5.5 1500 274.9
22:50:05.081 INFO ProgressMeter - chr10:32039325 5.6 1550 274.8
22:50:15.899 INFO ProgressMeter - chr10:43113415 5.8 1590 273.2
22:50:28.924 INFO ProgressMeter - chr10:43117556 6.0 1630 270.0
22:50:42.080 INFO ProgressMeter - chr10:62091946 6.3 1690 270.1
22:50:53.560 INFO ProgressMeter - chr10:68651844 6.4 1730 268.3
22:51:05.159 INFO ProgressMeter - chr10:87928748 6.6 1790 269.5
22:51:16.254 INFO ProgressMeter - chr10:101770473 6.8 1840 269.6
22:51:27.728 INFO ProgressMeter - chr10:110577814 7.0 1910 272.2
22:51:39.942 INFO ProgressMeter - chr10:110602804 7.2 1950 270.0
22:51:53.707 INFO ProgressMeter - chr10:121481770 7.5 2000 268.4
22:52:04.026 INFO ProgressMeter - chr10:121538682 7.6 2040 267.6
22:52:14.523 INFO ProgressMeter - chr11:17720900 7.8 2090 268.0
22:52:25.050 INFO ProgressMeter - chr11:64370223 8.0 2150 269.7
22:52:35.332 INFO ProgressMeter - chr11:69646623 8.1 2210 271.4
22:52:46.955 INFO ProgressMeter - chr11:69700007 8.3 2260 271.1
22:52:57.225 INFO ProgressMeter - chr11:69708787 8.5 2300 270.3
22:53:07.547 INFO ProgressMeter - chr11:69777315 8.7 2350 270.7
22:53:18.192 INFO ProgressMeter - chr11:69811667 8.9 2370 267.5
22:53:30.177 INFO ProgressMeter - chr11:76496216 9.1 2420 267.2
22:53:42.682 INFO ProgressMeter - chr11:77358993 9.3 2470 266.5
22:53:53.240 INFO ProgressMeter - chr11:77439651 9.4 2510 265.8
22:54:04.161 INFO ProgressMeter - chr11:101128021 9.6 2570 267.0
22:54:17.428 INFO ProgressMeter - chr11:102325327 9.8 2600 264.1
22:54:27.978 INFO ProgressMeter - chr11:108315821 10.0 2660 265.4
22:54:38.510 INFO ProgressMeter - chr11:118472904 10.2 2720 266.7
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22:55:00.497 INFO ProgressMeter - chr11:118506561 10.6 2800 265.1
22:55:15.386 INFO ProgressMeter - chr11:125629389 10.8 2850 263.6
22:55:26.788 INFO ProgressMeter - chr11:128458875 11.0 2900 263.6
22:55:37.182 INFO ProgressMeter - chr11:128460022 11.2 2910 260.4
22:55:47.608 INFO ProgressMeter - chr11:128587486 11.3 2950 259.9
22:55:58.121 INFO ProgressMeter - chr11:128812603 11.5 2990 259.5
22:56:08.870 INFO ProgressMeter - chr12:354134 11.7 3040 259.8
22:56:20.831 INFO ProgressMeter - chr12:4375229 11.9 3100 260.5
22:56:32.784 INFO ProgressMeter - chr12:4440052 12.1 3140 259.5
22:56:44.788 INFO ProgressMeter - chr12:6587382 12.3 3190 259.3
22:56:55.194 INFO ProgressMeter - chr12:6602467 12.5 3230 258.9
22:57:09.134 INFO ProgressMeter - chr12:11856768 12.7 3270 257.3
22:57:22.030 INFO ProgressMeter - chr12:11862513 12.9 3310 256.1
22:57:33.149 INFO ProgressMeter - chr12:11866242 13.1 3340 254.8
22:57:45.270 INFO ProgressMeter - chr12:12115295 13.3 3370 253.2
22:57:55.818 INFO ProgressMeter - chr12:18647991 13.5 3430 254.3
22:58:10.236 INFO ProgressMeter - chr12:45730042 13.7 3490 254.3
22:58:21.650 INFO ProgressMeter - chr12:45904932 13.9 3540 254.4
22:58:31.716 INFO ProgressMeter - chr12:49032724 14.1 3580 254.2
22:58:44.073 INFO ProgressMeter - chr12:49038639 14.3 3610 252.6
22:58:55.597 INFO ProgressMeter - chr12:49050613 14.5 3660 252.7
22:59:06.329 INFO ProgressMeter - chr12:51981069 14.7 3710 253.1
22:59:17.527 INFO ProgressMeter - chr12:56099836 14.8 3770 253.9
22:59:30.719 INFO ProgressMeter - chr12:57464072 15.1 3820 253.5
22:59:40.935 INFO ProgressMeter - chr12:57750436 15.2 3870 254.0
22:59:51.464 INFO ProgressMeter - chr12:68836530 15.4 3930 255.0
23:00:02.883 INFO ProgressMeter - chr12:111446844 15.6 3990 255.7
23:00:15.318 INFO ProgressMeter - chr12:120993676 15.8 4050 256.2
23:00:27.274 INFO ProgressMeter - chr12:132649804 16.0 4100 256.1
23:00:39.988 INFO ProgressMeter - chr13:20983419 16.2 4160 256.4
23:00:50.098 INFO ProgressMeter - chr13:21676821 16.4 4200 256.3
23:01:00.171 INFO ProgressMeter - chr13:28015588 16.6 4260 257.3
23:01:13.373 INFO ProgressMeter - chr13:28386106 16.8 4320 257.5
23:01:27.893 INFO ProgressMeter - chr13:28389049 17.0 4340 255.0
23:01:38.839 INFO ProgressMeter - chr13:32336740 17.2 4390 255.2
23:01:50.740 INFO ProgressMeter - chr13:32379315 17.4 4440 255.2
23:02:00.894 INFO ProgressMeter - chr13:48479996 17.6 4500 256.1
23:02:11.158 INFO ProgressMeter - chr13:102201277 17.7 4560 257.0
23:02:22.035 INFO ProgressMeter - chr13:109762154 17.9 4610 257.2
23:02:32.440 INFO ProgressMeter - chr13:113307937 18.1 4660 257.5
23:02:43.677 INFO ProgressMeter - chr14:25381560 18.3 4700 257.1
23:02:54.172 INFO ProgressMeter - chr14:37590249 18.5 4750 257.3
23:03:06.196 INFO ProgressMeter - chr14:37599303 18.7 4800 257.3
23:03:18.088 INFO ProgressMeter - chr14:81143943 18.9 4860 257.7
23:03:29.153 INFO ProgressMeter - chr14:95124670 19.0 4910 257.9
23:03:39.282 INFO ProgressMeter - chr14:104775690 19.2 4960 258.2
23:03:54.004 INFO ProgressMeter - chr15:34347815 19.5 5000 257.0
23:04:06.059 INFO ProgressMeter - chr15:40698755 19.7 5040 256.4
23:04:18.158 INFO ProgressMeter - chr15:41742544 19.9 5090 256.3
23:04:28.828 INFO ProgressMeter - chr15:44715643 20.0 5130 256.0
23:04:40.351 INFO ProgressMeter - chr15:66436744 20.2 5190 256.6
23:04:51.249 INFO ProgressMeter - chr15:87929189 20.4 5240 256.7
23:05:02.551 INFO ProgressMeter - chr15:89247646 20.6 5290 256.8
23:05:12.905 INFO ProgressMeter - chr15:90091551 20.8 5350 257.6
23:05:22.969 INFO ProgressMeter - chr15:92941873 20.9 5400 257.9
23:05:34.863 INFO ProgressMeter - chr15:98899475 21.1 5460 258.3
23:05:45.349 INFO ProgressMeter - chr16:346146 21.3 5510 258.6
23:05:57.214 INFO ProgressMeter - chr16:2083693 21.5 5570 259.0
23:06:08.096 INFO ProgressMeter - chr16:3584767 21.7 5650 260.5
23:06:18.387 INFO ProgressMeter - chr16:3608470 21.9 5690 260.3
23:06:29.461 INFO ProgressMeter - chr16:3738569 22.0 5730 259.9
23:06:41.764 INFO ProgressMeter - chr16:9764839 22.3 5780 259.8
23:06:53.333 INFO ProgressMeter - chr16:13948299 22.4 5830 259.8
23:07:03.986 INFO ProgressMeter - chr16:30118426 22.6 5880 259.9
23:07:14.227 INFO ProgressMeter - chr16:56823705 22.8 5940 260.6
23:07:24.433 INFO ProgressMeter - chr16:68810195 23.0 5990 260.9
23:07:36.944 INFO ProgressMeter - chr16:72794325 23.2 6030 260.2
23:07:47.624 INFO ProgressMeter - chr16:72798533 23.3 6060 259.5
23:07:59.138 INFO ProgressMeter - chr16:81858261 23.5 6100 259.1
23:08:11.663 INFO ProgressMeter - chr16:89281618 23.7 6160 259.4
23:08:21.799 INFO ProgressMeter - chr16:89286037 23.9 6190 258.8
23:08:33.101 INFO ProgressMeter - chr16:89810927 24.1 6260 259.7
23:08:45.303 INFO ProgressMeter - chr17:7675290 24.3 6310 259.6
23:08:56.098 INFO ProgressMeter - chr17:8086168 24.5 6370 260.1
23:09:07.187 INFO ProgressMeter - chr17:16073560 24.7 6430 260.6
23:09:17.870 INFO ProgressMeter - chr17:17225976 24.9 6490 261.1
23:09:28.947 INFO ProgressMeter - chr17:31261709 25.0 6560 262.0
23:09:39.581 INFO ProgressMeter - chr17:35103252 25.2 6620 262.5
23:09:50.858 INFO ProgressMeter - chr17:39526178 25.4 6670 262.6
23:10:02.702 INFO ProgressMeter - chr17:39724865 25.6 6730 262.9
23:10:13.188 INFO ProgressMeter - chr17:40406382 25.8 6790 263.4
23:10:23.571 INFO ProgressMeter - chr17:42309375 25.9 6860 264.4
23:10:35.356 INFO ProgressMeter - chr17:43090984 26.1 6930 265.1
23:10:45.547 INFO ProgressMeter - chr17:43528141 26.3 6970 264.9
23:10:56.621 INFO ProgressMeter - chr17:43534992 26.5 7010 264.5
23:11:07.796 INFO ProgressMeter - chr17:43540181 26.7 7050 264.2
23:11:22.513 INFO ProgressMeter - chr17:43544045 26.9 7080 262.9
23:11:33.145 INFO ProgressMeter - chr17:45290488 27.1 7120 262.7
23:11:44.189 INFO ProgressMeter - chr17:58695030 27.3 7170 262.7
23:11:57.484 INFO ProgressMeter - chr17:59947505 27.5 7250 263.5
23:12:08.225 INFO ProgressMeter - chr17:63929768 27.7 7300 263.6
23:12:19.510 INFO ProgressMeter - chr17:68529997 27.9 7350 263.6
23:12:30.413 INFO ProgressMeter - chr17:80908911 28.1 7410 264.1
23:12:41.257 INFO ProgressMeter - chr18:25673224 28.2 7470 264.5
23:12:52.357 INFO ProgressMeter - chr18:44951026 28.4 7520 264.5
23:13:02.496 INFO ProgressMeter - chr18:47870473 28.6 7560 264.4
23:13:13.111 INFO ProgressMeter - chr18:63318487 28.8 7620 264.8
23:13:23.294 INFO ProgressMeter - chr19:2210398 28.9 7680 265.3
23:13:34.920 INFO ProgressMeter - chr19:4054354 29.1 7740 265.6
23:13:45.527 INFO ProgressMeter - chr19:5225754 29.3 7800 266.1
23:13:56.303 INFO ProgressMeter - chr19:7170645 29.5 7860 266.5
23:14:07.649 INFO ProgressMeter - chr19:10154291 29.7 7900 266.1
23:14:17.807 INFO ProgressMeter - chr19:10985271 29.9 7950 266.3
23:14:28.858 INFO ProgressMeter - chr19:12940584 30.0 8010 266.7
23:14:39.343 INFO ProgressMeter - chr19:15165883 30.2 8050 266.5
23:14:50.797 INFO ProgressMeter - chr19:15191958 30.4 8100 266.4
23:15:01.195 INFO ProgressMeter - chr19:15265373 30.6 8150 266.6
23:15:12.748 INFO ProgressMeter - chr19:18156178 30.8 8190 266.2
23:15:25.199 INFO ProgressMeter - chr19:29819201 31.0 8260 266.7
23:15:37.385 INFO ProgressMeter - chr19:35723729 31.2 8320 266.9
23:15:48.377 INFO ProgressMeter - chr19:35737634 31.4 8370 266.9
23:15:59.914 INFO ProgressMeter - chr19:41220634 31.6 8430 267.2
23:16:15.403 INFO ProgressMeter - chr19:41261585 31.8 8470 266.3
23:16:25.510 INFO ProgressMeter - chr19:42293933 32.0 8520 266.4
23:16:36.717 INFO ProgressMeter - chr19:45369068 32.2 8580 266.7
23:16:48.322 INFO ProgressMeter - chr19:45421176 32.4 8640 267.0
23:17:00.100 INFO ProgressMeter - chr19:52222097 32.6 8710 267.5
23:17:13.949 INFO ProgressMeter - chr2:15943986 32.8 8750 266.9
23:17:24.823 INFO ProgressMeter - chr2:25234277 33.0 8800 266.9
23:17:37.186 INFO ProgressMeter - chr2:25743042 33.2 8850 266.8
23:17:49.202 INFO ProgressMeter - chr2:29204807 33.4 8900 266.7
23:18:02.102 INFO ProgressMeter - chr2:29225373 33.6 8930 265.9
23:18:14.145 INFO ProgressMeter - chr2:29510990 33.8 8970 265.5
23:18:24.207 INFO ProgressMeter - chr2:42326152 34.0 9030 265.9
23:18:40.919 INFO ProgressMeter - chr2:47466656 34.2 9080 265.2
23:18:51.584 INFO ProgressMeter - chr2:47800653 34.4 9120 265.0
23:19:02.559 INFO ProgressMeter - chr2:61495453 34.6 9190 265.6
23:19:14.000 INFO ProgressMeter - chr2:98552784 34.8 9230 265.3
23:19:25.431 INFO ProgressMeter - chr2:108765297 35.0 9290 265.6
23:19:35.754 INFO ProgressMeter - chr2:111126872 35.2 9340 265.7
23:19:50.457 INFO ProgressMeter - chr2:111142331 35.4 9360 264.4
23:20:03.259 INFO ProgressMeter - chr2:113224196 35.6 9400 264.0
23:20:19.837 INFO ProgressMeter - chr2:113227090 35.9 9420 262.5
23:20:30.576 INFO ProgressMeter - chr2:113230652 36.1 9450 262.0
23:20:41.580 INFO ProgressMeter - chr2:113232647 36.2 9470 261.3
23:20:53.743 INFO ProgressMeter - chr2:113234835 36.5 9490 260.3
23:21:05.250 INFO ProgressMeter - chr2:127289416 36.6 9540 260.4
23:21:15.635 INFO ProgressMeter - chr2:140492606 36.8 9600 260.8
23:21:27.173 INFO ProgressMeter - chr2:140922964 37.0 9660 261.0
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23:22:09.128 INFO ProgressMeter - chr2:211702144 37.7 9890 262.3
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23:22:32.174 INFO ProgressMeter - chr2:222203279 38.1 9970 261.7
23:22:42.320 INFO ProgressMeter - chr2:222207268 38.3 10000 261.4
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23:23:05.969 INFO ProgressMeter - chr2:222216674 38.7 10060 260.3
23:23:18.661 INFO ProgressMeter - chr2:222294290 38.9 10100 259.9
23:23:30.419 INFO ProgressMeter - chr2:226796985 39.1 10150 259.8
23:23:41.584 INFO ProgressMeter - chr20:31694198 39.2 10200 259.9
23:23:51.946 INFO ProgressMeter - chr20:32436437 39.4 10240 259.8
23:24:02.243 INFO ProgressMeter - chr20:41029429 39.6 10300 260.1
23:24:12.672 INFO ProgressMeter - chr20:42472264 39.8 10360 260.5
23:24:24.242 INFO ProgressMeter - chr20:47651043 40.0 10410 260.5
23:24:34.966 INFO ProgressMeter - chr20:56386255 40.1 10450 260.4
23:24:45.252 INFO ProgressMeter - chr20:63706997 40.3 10500 260.5
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23:25:07.680 INFO ProgressMeter - chr21:41464721 40.7 10590 260.3
23:25:22.593 INFO ProgressMeter - chr21:41490311 40.9 10630 259.7
23:25:36.410 INFO ProgressMeter - chr21:41492728 41.2 10650 258.7
23:25:46.860 INFO ProgressMeter - chr21:41500103 41.3 10680 258.4
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23:26:08.381 INFO ProgressMeter - chr21:41507492 41.7 10740 257.6
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23:26:48.772 INFO ProgressMeter - chr22:28711907 42.4 10920 257.7
23:26:59.542 INFO ProgressMeter - chr22:29284293 42.5 10980 258.1
23:27:10.351 INFO ProgressMeter - chr22:29297825 42.7 11010 257.7
23:27:21.819 INFO ProgressMeter - chr22:41127485 42.9 11060 257.7
23:27:31.841 INFO ProgressMeter - chr22:41177594 43.1 11110 257.9
23:27:42.748 INFO ProgressMeter - chr3:10081390 43.3 11170 258.2
23:27:57.109 INFO ProgressMeter - chr3:12354817 43.5 11220 257.9
23:28:09.662 INFO ProgressMeter - chr3:12359238 43.7 11250 257.3
23:28:21.837 INFO ProgressMeter - chr3:12362404 43.9 11270 256.6
23:28:33.931 INFO ProgressMeter - chr3:12366915 44.1 11300 256.1
23:28:45.519 INFO ProgressMeter - chr3:12371268 44.3 11330 255.7
23:28:58.119 INFO ProgressMeter - chr3:12375997 44.5 11360 255.1
23:29:09.110 INFO ProgressMeter - chr3:12586004 44.7 11400 255.0
23:29:20.155 INFO ProgressMeter - chr3:12662879 44.9 11440 254.8
23:29:31.814 INFO ProgressMeter - chr3:41233339 45.1 11510 255.3
23:29:43.509 INFO ProgressMeter - chr3:47122098 45.3 11560 255.3
23:29:54.820 INFO ProgressMeter - chr3:49687413 45.5 11610 255.3
23:30:05.460 INFO ProgressMeter - chr3:52402286 45.6 11660 255.4
23:30:16.529 INFO ProgressMeter - chr3:52609823 45.8 11720 255.7
23:30:26.915 INFO ProgressMeter - chr3:71000970 46.0 11780 256.1
23:30:36.943 INFO ProgressMeter - chr3:89341914 46.2 11830 256.2
23:30:49.622 INFO ProgressMeter - chr3:134951924 46.4 11890 256.3
23:31:01.248 INFO ProgressMeter - chr3:136443266 46.6 11950 256.6
23:31:11.272 INFO ProgressMeter - chr3:138721926 46.7 12010 256.9
23:31:23.060 INFO ProgressMeter - chr3:142513499 46.9 12070 257.1
23:31:34.104 INFO ProgressMeter - chr3:170293381 47.1 12130 257.4
23:31:44.966 INFO ProgressMeter - chr3:181710213 47.3 12190 257.7
23:31:55.280 INFO ProgressMeter - chr3:185428655 47.5 12240 257.8
23:32:08.194 INFO ProgressMeter - chr3:186047842 47.7 12280 257.5
23:32:20.157 INFO ProgressMeter - chr3:189789799 47.9 12340 257.7
23:32:30.540 INFO ProgressMeter - chr3:196073453 48.1 12400 258.0
23:32:42.404 INFO ProgressMeter - chr4:1807127 48.3 12470 258.4
23:32:54.300 INFO ProgressMeter - chr4:24554704 48.5 12540 258.8
23:33:04.628 INFO ProgressMeter - chr4:54270631 48.6 12590 258.9
23:33:15.394 INFO ProgressMeter - chr4:54703722 48.8 12640 259.0
23:33:27.120 INFO ProgressMeter - chr4:54737173 49.0 12670 258.5
23:33:37.414 INFO ProgressMeter - chr4:65367355 49.2 12730 258.9
23:33:48.731 INFO ProgressMeter - chr4:80285144 49.4 12790 259.1
23:33:58.880 INFO ProgressMeter - chr4:105235256 49.5 12840 259.2
23:34:10.182 INFO ProgressMeter - chr4:105241868 49.7 12880 259.0
23:34:21.152 INFO ProgressMeter - chr4:122843484 49.9 12920 258.9
23:34:32.069 INFO ProgressMeter - chr4:152352630 50.1 12990 259.3
23:34:42.943 INFO ProgressMeter - chr4:186600143 50.3 13040 259.4
23:34:53.956 INFO ProgressMeter - chr4:186619662 50.5 13080 259.2
23:35:05.526 INFO ProgressMeter - chr4:186707949 50.6 13120 259.0
23:35:17.913 INFO ProgressMeter - chr5:2879220 50.9 13170 259.0
23:35:29.222 INFO ProgressMeter - chr5:38964790 51.0 13240 259.4
23:35:39.868 INFO ProgressMeter - chr5:56815572 51.2 13310 259.9
23:35:51.742 INFO ProgressMeter - chr5:58457179 51.4 13360 259.8
23:36:02.045 INFO ProgressMeter - chr5:80741462 51.6 13430 260.3
23:36:13.575 INFO ProgressMeter - chr5:112828902 51.8 13510 260.9
23:36:25.773 INFO ProgressMeter - chr5:112842891 52.0 13550 260.7
23:36:37.113 INFO ProgressMeter - chr5:132604880 52.2 13600 260.7
23:36:48.364 INFO ProgressMeter - chr5:142630853 52.4 13660 260.9
23:36:59.589 INFO ProgressMeter - chr5:149507006 52.5 13700 260.7
23:37:10.023 INFO ProgressMeter - chr5:150080134 52.7 13750 260.8
23:37:21.863 INFO ProgressMeter - chr5:150139224 52.9 13800 260.8
23:37:33.255 INFO ProgressMeter - chr5:161701496 53.1 13850 260.8
23:37:45.082 INFO ProgressMeter - chr5:177090759 53.3 13890 260.6
23:38:00.643 INFO ProgressMeter - chr5:177135892 53.6 13930 260.1
23:38:12.485 INFO ProgressMeter - chr5:177273670 53.8 13970 259.8
23:38:23.233 INFO ProgressMeter - chr5:177515165 53.9 14020 259.9
23:38:33.738 INFO ProgressMeter - chr5:180629257 54.1 14070 260.0
23:38:44.526 INFO ProgressMeter - chr6:20451963 54.3 14130 260.2
23:38:55.194 INFO ProgressMeter - chr6:26044841 54.5 14180 260.3
23:39:09.075 INFO ProgressMeter - chr6:29944498 54.7 14230 260.1
23:39:19.527 INFO ProgressMeter - chr6:30711410 54.9 14270 260.0
23:39:29.974 INFO ProgressMeter - chr6:32204135 55.1 14320 260.1
23:39:42.695 INFO ProgressMeter - chr6:33319722 55.3 14360 259.8
23:39:52.705 INFO ProgressMeter - chr6:37170574 55.4 14410 260.0
23:40:03.984 INFO ProgressMeter - chr6:43770705 55.6 14480 260.3
23:40:14.361 INFO ProgressMeter - chr6:93410646 55.8 14530 260.4
23:40:24.828 INFO ProgressMeter - chr6:112061071 56.0 14580 260.5
23:40:35.851 INFO ProgressMeter - chr6:117321183 56.2 14620 260.4
23:40:48.290 INFO ProgressMeter - chr6:117325042 56.4 14650 259.9
23:41:00.770 INFO ProgressMeter - chr6:117331934 56.6 14690 259.7
23:41:12.649 INFO ProgressMeter - chr6:117338919 56.8 14740 259.7
23:41:23.049 INFO ProgressMeter - chr6:117387914 56.9 14780 259.6
23:41:35.233 INFO ProgressMeter - chr6:135204853 57.1 14830 259.5
23:41:45.849 INFO ProgressMeter - chr6:135208601 57.3 14860 259.2
23:41:58.256 INFO ProgressMeter - chr6:135212740 57.5 14890 258.8
23:42:08.769 INFO ProgressMeter - chr6:135216799 57.7 14920 258.6
23:42:19.967 INFO ProgressMeter - chr6:149662043 57.9 14970 258.6
23:42:31.231 INFO ProgressMeter - chr6:151768996 58.1 15010 258.5
23:42:42.196 INFO ProgressMeter - chr6:152376495 58.3 15060 258.5
23:42:52.519 INFO ProgressMeter - chr6:157190036 58.4 15100 258.4
23:43:03.829 INFO ProgressMeter - chr6:161073464 58.6 15140 258.3
23:43:13.945 INFO ProgressMeter - chr6:163534980 58.8 15200 258.6
23:43:24.440 INFO ProgressMeter - chr7:2944210 59.0 15250 258.6
23:43:38.577 INFO ProgressMeter - chr7:13894394 59.2 15310 258.6
23:43:51.642 INFO ProgressMeter - chr7:13909494 59.4 15340 258.2
23:44:01.836 INFO ProgressMeter - chr7:13934096 59.6 15360 257.8
23:44:12.928 INFO ProgressMeter - chr7:13939222 59.8 15400 257.7
23:44:23.114 INFO ProgressMeter - chr7:13944082 59.9 15430 257.4
23:44:33.646 INFO ProgressMeter - chr7:13946595 60.1 15450 257.0
23:44:44.033 INFO ProgressMeter - chr7:13950091 60.3 15480 256.8
23:44:59.650 INFO ProgressMeter - chr7:13953632 60.5 15510 256.2
23:45:10.863 INFO ProgressMeter - chr7:13959432 60.7 15550 256.0
23:45:26.131 INFO ProgressMeter - chr7:13963990 61.0 15580 255.4
23:45:37.173 INFO ProgressMeter - chr7:13969244 61.2 15620 255.3
23:45:48.022 INFO ProgressMeter - chr7:13970377 61.4 15630 254.7
23:46:00.793 INFO ProgressMeter - chr7:13974344 61.6 15660 254.4
23:46:12.193 INFO ProgressMeter - chr7:13976705 61.8 15680 253.9
23:46:22.503 INFO ProgressMeter - chr7:13980916 61.9 15710 253.7
23:46:35.060 INFO ProgressMeter - chr7:13988133 62.1 15750 253.5
23:46:46.385 INFO ProgressMeter - chr7:41690097 62.3 15770 253.0
23:46:58.273 INFO ProgressMeter - chr7:55153646 62.5 15820 253.0
23:47:10.696 INFO ProgressMeter - chr7:55167787 62.7 15860 252.8
23:47:21.367 INFO ProgressMeter - chr7:55173027 62.9 15890 252.6
23:47:34.071 INFO ProgressMeter - chr7:55179604 63.1 15930 252.4
23:47:47.137 INFO ProgressMeter - chr7:55205537 63.3 15970 252.1
23:47:57.825 INFO ProgressMeter - chr7:81725888 63.5 16030 252.4
23:48:08.387 INFO ProgressMeter - chr7:92686936 63.7 16080 252.5
23:48:19.772 INFO ProgressMeter - chr7:102204370 63.9 16140 252.6
23:48:31.142 INFO ProgressMeter - chr7:106874698 64.1 16190 252.7
23:48:42.178 INFO ProgressMeter - chr7:116773120 64.3 16240 252.7
23:48:53.475 INFO ProgressMeter - chr7:140752633 64.4 16290 252.8
23:49:04.640 INFO ProgressMeter - chr7:140793554 64.6 16340 252.8
23:49:15.471 INFO ProgressMeter - chr7:142944321 64.8 16400 253.0
23:49:27.437 INFO ProgressMeter - chr7:152148585 65.0 16470 253.3
23:49:40.908 INFO ProgressMeter - chr7:152177225 65.2 16520 253.2
23:49:51.249 INFO ProgressMeter - chr7:152238806 65.4 16570 253.3
23:50:01.591 INFO ProgressMeter - chr8:23682602 65.6 16630 253.6
23:50:14.515 INFO ProgressMeter - chr8:32646730 65.8 16690 253.7
23:50:27.089 INFO ProgressMeter - chr8:37697143 66.0 16730 253.5
23:50:37.644 INFO ProgressMeter - chr8:37839513 66.2 16780 253.5
23:50:47.997 INFO ProgressMeter - chr8:38428349 66.4 16820 253.5
23:50:58.913 INFO ProgressMeter - chr8:41934344 66.5 16860 253.4
23:51:10.030 INFO ProgressMeter - chr8:47785166 66.7 16910 253.4
23:51:21.170 INFO ProgressMeter - chr8:47885942 66.9 16970 253.6
23:51:32.966 INFO ProgressMeter - chr8:55947616 67.1 17040 253.9
23:51:43.657 INFO ProgressMeter - chr8:68134057 67.3 17100 254.2
23:51:54.483 INFO ProgressMeter - chr8:92011000 67.5 17160 254.4
23:52:05.348 INFO ProgressMeter - chr8:127735568 67.6 17200 254.3
23:52:16.078 INFO ProgressMeter - chr8:127745289 67.8 17240 254.2
23:52:27.871 INFO ProgressMeter - chr9:5029781 68.0 17300 254.3
23:52:38.702 INFO ProgressMeter - chr9:5549437 68.2 17360 254.5
23:52:48.731 INFO ProgressMeter - chr9:8518181 68.4 17410 254.7
23:53:00.393 INFO ProgressMeter - chr9:22006231 68.6 17460 254.7
23:53:11.398 INFO ProgressMeter - chr9:83970175 68.7 17520 254.9
23:53:28.681 INFO ProgressMeter - chr9:84742931 69.0 17570 254.5
23:53:39.655 INFO ProgressMeter - chr9:84812613 69.2 17600 254.3
23:53:57.807 INFO ProgressMeter - chr9:84861038 69.5 17630 253.6
23:54:12.908 INFO ProgressMeter - chr9:84864902 69.8 17660 253.1
23:54:23.630 INFO ProgressMeter - chr9:84873501 69.9 17690 252.9
23:54:33.823 INFO ProgressMeter - chr9:84877004 70.1 17720 252.7
23:54:45.067 INFO ProgressMeter - chr9:85023727 70.3 17750 252.5
23:54:56.517 INFO ProgressMeter - chr9:85026970 70.5 17770 252.1
23:55:09.348 INFO ProgressMeter - chr9:95461854 70.7 17830 252.2
23:55:19.401 INFO ProgressMeter - chr9:99146577 70.9 17880 252.3
23:55:32.145 INFO ProgressMeter - chr9:130884515 71.1 17940 252.4
23:55:43.360 INFO ProgressMeter - chr9:132903649 71.3 17980 252.3
23:55:54.833 INFO ProgressMeter - chr9:136503180 71.5 18030 252.3
23:56:05.534 INFO ProgressMeter - chr9:136670167 71.6 18090 252.5
23:56:15.871 INFO ProgressMeter - chrX:40063044 71.8 18150 252.7
23:56:27.389 INFO ProgressMeter - chrX:45063420 72.0 18200 252.7
23:56:37.511 INFO ProgressMeter - chrX:47181213 72.2 18240 252.7
23:56:50.704 INFO ProgressMeter - chrX:49029058 72.4 18290 252.6
23:57:06.541 INFO ProgressMeter - chrX:49035425 72.7 18320 252.1
23:57:19.256 INFO ProgressMeter - chrX:49040453 72.9 18350 251.8
23:57:30.289 INFO ProgressMeter - chrX:53210825 73.1 18390 251.7
23:57:41.122 INFO ProgressMeter - chrX:53405750 73.2 18430 251.6
23:57:53.296 INFO ProgressMeter - chrX:64191340 73.4 18470 251.5
23:58:04.727 INFO ProgressMeter - chrX:67545630 73.6 18490 251.1
23:58:15.977 INFO ProgressMeter - chrX:67721831 73.8 18540 251.1
23:58:26.682 INFO ProgressMeter - chrX:71130168 74.0 18590 251.2
23:58:38.632 INFO ProgressMeter - chrX:71367497 74.2 18620 250.9
23:58:49.440 INFO ProgressMeter - chrX:71423115 74.4 18660 250.9
23:59:02.591 INFO ProgressMeter - chrX:77681657 74.6 18720 250.9
23:59:13.336 INFO ProgressMeter - chrX:101390546 74.8 18770 251.0
23:59:23.695 INFO ProgressMeter - chrX:124057864 75.0 18820 251.1
23:59:36.266 INFO ProgressMeter - chrX:130014419 75.2 18860 250.9
23:59:46.447 INFO ProgressMeter - chrX:130055852 75.3 18890 250.8
23:59:50.364 INFO Mutect2 - 947514 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
226 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
947740 total reads filtered out of 150018269 reads processed
23:59:50.364 INFO ProgressMeter - chrY:19773323 75.4 18946 251.3
23:59:50.364 INFO ProgressMeter - Traversal complete. Processed 18946 total regions in 75.4 minutes.
23:59:50.381 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 9.403492132
23:59:50.381 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 432.71250605100005
23:59:50.381 INFO SmithWatermanAligner - Total compute time in native Smith-Waterman : 15.20 sec
23:59:50.382 INFO Mutect2 - Shutting down engine
[June 8, 2026 at 11:59:50 PM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 75.40 minutes.
Runtime.totalMemory()=3296722944
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 LS0880_tumor.bam --tumor-sample LS0880 -L TST500C_manifest.bed -O LS0880.mutect2.raw.vcf.gz --native-pair-hmm-threads 4 --max-mnp-distance 0 --germline-resource af-only-gnomad.hg38.vcf.gz
23:59:51.747 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
23:59:51.865 INFO FilterMutectCalls - ------------------------------------------------------------
23:59:51.867 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.5.0.0
23:59:51.867 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:59:51.867 INFO FilterMutectCalls - Executing as ?@nf-bbf9165f87084e3e9d333c2b1e913cfb-5a867-v46zv on Linux v6.12.88 amd64
23:59:51.867 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
23:59:51.867 INFO FilterMutectCalls - Start Date/Time: June 8, 2026 at 11:59:51 PM GMT
23:59:51.867 INFO FilterMutectCalls - ------------------------------------------------------------
23:59:51.867 INFO FilterMutectCalls - ------------------------------------------------------------
23:59:51.868 INFO FilterMutectCalls - HTSJDK Version: 4.1.0
23:59:51.868 INFO FilterMutectCalls - Picard Version: 3.1.1
23:59:51.868 INFO FilterMutectCalls - Built for Spark Version: 3.5.0
23:59:51.868 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:59:51.868 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:59:51.868 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:59:51.869 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:59:51.869 INFO FilterMutectCalls - Deflater: IntelDeflater
23:59:51.869 INFO FilterMutectCalls - Inflater: IntelInflater
23:59:51.869 INFO FilterMutectCalls - GCS max retries/reopens: 20
23:59:51.869 INFO FilterMutectCalls - Requester pays: disabled
23:59:51.869 INFO FilterMutectCalls - Initializing engine
23:59:52.042 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.4jR2jrxr2i/LS0880.mutect2.raw.vcf.gz
23:59:52.152 INFO FilterMutectCalls - Done initializing engine
23:59:52.207 INFO ProgressMeter - Starting traversal
23:59:52.207 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
23:59:52.208 INFO FilterMutectCalls - Starting pass 0 through the variants
23:59:54.314 INFO FilterMutectCalls - Finished pass 0 through the variants
23:59:57.460 INFO FilterMutectCalls - Starting pass 1 through the variants
23:59:59.933 INFO FilterMutectCalls - Finished pass 1 through the variants
00:00:00.794 INFO FilterMutectCalls - Starting pass 2 through the variants
00:00:02.536 INFO ProgressMeter - chr6:12059721 0.2 8000 46489.1
00:00:03.230 INFO FilterMutectCalls - Finished pass 2 through the variants
00:00:03.232 INFO FilterMutectCalls - Starting pass 3 through the variants
00:00:05.267 INFO FilterMutectCalls - Finished pass 3 through the variants
00:00:05.272 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
00:00:05.272 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
00:00:05.272 INFO ProgressMeter - chr6:29943287 0.2 11840 54374.3
00:00:05.272 INFO ProgressMeter - Traversal complete. Processed 11840 total variants in 0.2 minutes.
00:00:05.282 INFO FilterMutectCalls - Shutting down engine
[June 9, 2026 at 12:00:05 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 0.23 minutes.
Runtime.totalMemory()=545259520
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 LS0880.mutect2.raw.vcf.gz --stats LS0880.mutect2.raw.vcf.gz.stats -O LS0880.mutect2.filtered.vcf.gz
00:00:06.441 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
00:00:06.536 INFO SelectVariants - ------------------------------------------------------------
00:00:06.539 INFO SelectVariants - The Genome Analysis Toolkit (GATK) v4.5.0.0
00:00:06.539 INFO SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
00:00:06.539 INFO SelectVariants - Executing as ?@nf-bbf9165f87084e3e9d333c2b1e913cfb-5a867-v46zv on Linux v6.12.88 amd64
00:00:06.539 INFO SelectVariants - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
00:00:06.539 INFO SelectVariants - Start Date/Time: June 9, 2026 at 12:00:06 AM GMT
00:00:06.539 INFO SelectVariants - ------------------------------------------------------------
00:00:06.540 INFO SelectVariants - ------------------------------------------------------------
00:00:06.540 INFO SelectVariants - HTSJDK Version: 4.1.0
00:00:06.540 INFO SelectVariants - Picard Version: 3.1.1
00:00:06.540 INFO SelectVariants - Built for Spark Version: 3.5.0
00:00:06.540 INFO SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
00:00:06.540 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
00:00:06.540 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
00:00:06.541 INFO SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
00:00:06.541 INFO SelectVariants - Deflater: IntelDeflater
00:00:06.541 INFO SelectVariants - Inflater: IntelInflater
00:00:06.541 INFO SelectVariants - GCS max retries/reopens: 20
00:00:06.541 INFO SelectVariants - Requester pays: disabled
00:00:06.541 INFO SelectVariants - Initializing engine
00:00:06.718 INFO FeatureManager - Using codec VCFCodec to read file file:///tmp/nxf.4jR2jrxr2i/LS0880.mutect2.filtered.vcf.gz
00:00:06.834 INFO SelectVariants - Done initializing engine
00:00:06.873 INFO ProgressMeter - Starting traversal
00:00:06.874 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
00:00:06.957 INFO ProgressMeter - chr5:112841059 0.0 2960 2220000.0
00:00:06.957 INFO ProgressMeter - Traversal complete. Processed 2960 total variants in 0.0 minutes.
00:00:06.967 INFO SelectVariants - Shutting down engine
[June 9, 2026 at 12:00:06 AM GMT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=494927872
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 LS0880.mutect2.filtered.vcf.gz --exclude-filtered true -O LS0880.mutect2.pass.vcf.gz