Downloading: s3://fsdx-algo-644019535899-us-west-2-an/references/hg38.fa
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/02/794f7555b116425cfe88a12543c0a2/.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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0917/LS0917_tumor.bam
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://lcgp-v1/analysis/20260410_LH01147_0003_A23LTV7LT4-30e8cff3-bb76-4fb1-8024-010a94113bb0/Logs_Intermediates/DragenCaller/LS0917/LS0917_tumor.bam.bai
Downloading: s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/02/794f7555b116425cfe88a12543c0a2/.command.run
==> STAGING COMPLETE (10 inputs)
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
23:30:39.710 INFO ProgressMeter - chr2:224511407 46.1 11860 257.3
23:30:52.906 INFO ProgressMeter - chr2:226798272 46.3 11900 257.0
23:31:03.135 INFO ProgressMeter - chr20:9580722 46.5 11940 256.9
23:31:14.892 INFO ProgressMeter - chr20:32435387 46.7 11990 256.9
23:31:25.774 INFO ProgressMeter - chr20:32799242 46.9 12040 257.0
23:31:36.390 INFO ProgressMeter - chr20:42080877 47.0 12110 257.5
23:31:46.917 INFO ProgressMeter - chr20:42780216 47.2 12160 257.6
23:31:59.276 INFO ProgressMeter - chr20:47652929 47.4 12210 257.5
23:32:09.480 INFO ProgressMeter - chr20:56373406 47.6 12250 257.4
23:32:19.889 INFO ProgressMeter - chr20:58903670 47.8 12300 257.5
23:32:31.221 INFO ProgressMeter - chr21:38380934 47.9 12360 257.8
23:32:41.399 INFO ProgressMeter - chr21:38400291 48.1 12400 257.7
23:32:53.122 INFO ProgressMeter - chr21:41465285 48.3 12440 257.5
23:33:08.252 INFO ProgressMeter - chr21:41490376 48.6 12480 257.0
23:33:18.575 INFO ProgressMeter - chr21:41492362 48.7 12500 256.5
23:33:29.083 INFO ProgressMeter - chr21:41498558 48.9 12530 256.2
23:33:40.140 INFO ProgressMeter - chr21:41502221 49.1 12560 255.8
23:33:50.643 INFO ProgressMeter - chr21:41505152 49.3 12590 255.5
23:34:01.751 INFO ProgressMeter - chr21:44229032 49.5 12630 255.4
23:34:12.353 INFO ProgressMeter - chr22:20997230 49.6 12690 255.7
23:34:25.958 INFO ProgressMeter - chr22:23290866 49.9 12750 255.7
23:34:36.628 INFO ProgressMeter - chr22:23314031 50.0 12770 255.2
23:34:46.732 INFO ProgressMeter - chr22:28725498 50.2 12830 255.5
23:34:59.787 INFO ProgressMeter - chr22:29285179 50.4 12890 255.6
23:35:11.310 INFO ProgressMeter - chr22:29654655 50.6 12930 255.5
23:35:22.313 INFO ProgressMeter - chr22:41135811 50.8 12990 255.7
23:35:34.557 INFO ProgressMeter - chr22:41178624 51.0 13050 255.9
23:35:44.712 INFO ProgressMeter - chr3:10081138 51.2 13110 256.2
23:35:57.317 INFO ProgressMeter - chr3:12353514 51.4 13170 256.3
23:36:10.695 INFO ProgressMeter - chr3:12356443 51.6 13200 255.8
23:36:22.475 INFO ProgressMeter - chr3:12360256 51.8 13230 255.4
23:36:32.981 INFO ProgressMeter - chr3:12362030 52.0 13250 254.9
23:36:46.514 INFO ProgressMeter - chr3:12366520 52.2 13290 254.6
23:36:59.237 INFO ProgressMeter - chr3:12369880 52.4 13320 254.1
23:37:11.411 INFO ProgressMeter - chr3:12373392 52.6 13350 253.7
23:37:23.168 INFO ProgressMeter - chr3:12377252 52.8 13380 253.3
23:37:34.757 INFO ProgressMeter - chr3:12405971 53.0 13410 253.0
23:37:44.929 INFO ProgressMeter - chr3:12615193 53.2 13450 252.9
23:37:55.405 INFO ProgressMeter - chr3:30671861 53.4 13490 252.9
23:38:05.937 INFO ProgressMeter - chr3:38138860 53.5 13540 253.0
23:38:16.090 INFO ProgressMeter - chr3:47019758 53.7 13580 252.9
23:38:28.177 INFO ProgressMeter - chr3:47120707 53.9 13620 252.7
23:38:41.424 INFO ProgressMeter - chr3:47123885 54.1 13650 252.2
23:38:53.354 INFO ProgressMeter - chr3:49891756 54.3 13710 252.4
23:39:03.842 INFO ProgressMeter - chr3:52403414 54.5 13750 252.3
23:39:16.032 INFO ProgressMeter - chr3:52609863 54.7 13810 252.5
23:39:27.411 INFO ProgressMeter - chr3:70972009 54.9 13870 252.7
23:39:38.138 INFO ProgressMeter - chr3:72841043 55.1 13920 252.8
23:39:49.582 INFO ProgressMeter - chr3:119905753 55.3 13970 252.8
23:40:01.692 INFO ProgressMeter - chr3:135201520 55.5 14020 252.8
23:40:14.544 INFO ProgressMeter - chr3:136473518 55.7 14070 252.7
23:40:26.336 INFO ProgressMeter - chr3:138704699 55.9 14120 252.7
23:40:37.553 INFO ProgressMeter - chr3:142466322 56.1 14180 253.0
23:40:48.430 INFO ProgressMeter - chr3:142560347 56.2 14250 253.4
23:40:58.677 INFO ProgressMeter - chr3:179166522 56.4 14310 253.7
23:41:09.934 INFO ProgressMeter - chr3:181708313 56.6 14370 253.9
23:41:22.144 INFO ProgressMeter - chr3:185443627 56.8 14430 254.1
23:41:33.292 INFO ProgressMeter - chr3:186047665 57.0 14460 253.8
23:41:45.560 INFO ProgressMeter - chr3:187729876 57.2 14520 253.9
23:41:57.116 INFO ProgressMeter - chr3:196055151 57.4 14580 254.1
23:42:08.194 INFO ProgressMeter - chr4:1792942 57.6 14640 254.3
23:42:18.969 INFO ProgressMeter - chr4:10967464 57.7 14700 254.6
23:42:29.420 INFO ProgressMeter - chr4:24527906 57.9 14760 254.8
23:42:39.517 INFO ProgressMeter - chr4:41746316 58.1 14800 254.8
23:42:51.701 INFO ProgressMeter - chr4:54277430 58.3 14850 254.8
23:43:03.425 INFO ProgressMeter - chr4:54699628 58.5 14900 254.8
23:43:17.034 INFO ProgressMeter - chr4:54732108 58.7 14930 254.3
23:43:27.775 INFO ProgressMeter - chr4:55107858 58.9 14970 254.2
23:43:38.508 INFO ProgressMeter - chr4:65643361 59.1 15020 254.3
23:43:50.008 INFO ProgressMeter - chr4:80286799 59.3 15070 254.3
23:44:01.244 INFO ProgressMeter - chr4:105235528 59.4 15120 254.3
23:44:13.366 INFO ProgressMeter - chr4:105241031 59.6 15160 254.1
23:44:26.650 INFO ProgressMeter - chr4:105275237 59.9 15190 253.7
23:44:37.084 INFO ProgressMeter - chr4:122892315 60.0 15250 254.0
23:44:49.082 INFO ProgressMeter - chr4:152352788 60.2 15320 254.3
23:45:00.194 INFO ProgressMeter - chr4:186599896 60.4 15370 254.3
23:45:10.750 INFO ProgressMeter - chr4:186618438 60.6 15410 254.3
23:45:22.292 INFO ProgressMeter - chr4:186636777 60.8 15450 254.1
23:45:33.185 INFO ProgressMeter - chr4:189396854 61.0 15480 253.9
23:45:43.692 INFO ProgressMeter - chr5:35876069 61.2 15530 253.9
23:45:54.290 INFO ProgressMeter - chr5:38971875 61.3 15590 254.2
23:46:05.245 INFO ProgressMeter - chr5:44376931 61.5 15660 254.6
23:46:16.903 INFO ProgressMeter - chr5:56885984 61.7 15710 254.6
23:46:28.502 INFO ProgressMeter - chr5:80665141 61.9 15780 254.9
23:46:39.641 INFO ProgressMeter - chr5:112738403 62.1 15860 255.4
23:46:49.885 INFO ProgressMeter - chr5:112839123 62.3 15900 255.4
23:47:02.720 INFO ProgressMeter - chr5:112843483 62.5 15940 255.2
23:47:13.241 INFO ProgressMeter - chr5:132579860 62.6 15980 255.1
23:47:24.448 INFO ProgressMeter - chr5:138824712 62.8 16040 255.3
23:47:36.082 INFO ProgressMeter - chr5:142665652 63.0 16100 255.4
23:47:47.194 INFO ProgressMeter - chr5:150054320 63.2 16140 255.3
23:47:58.428 INFO ProgressMeter - chr5:150121202 63.4 16190 255.4
23:48:09.324 INFO ProgressMeter - chr5:150401893 63.6 16240 255.4
23:48:20.364 INFO ProgressMeter - chr5:171400846 63.8 16290 255.5
23:48:31.058 INFO ProgressMeter - chr5:177090388 63.9 16320 255.2
23:48:48.812 INFO ProgressMeter - chr5:177135458 64.2 16370 254.8
23:49:00.266 INFO ProgressMeter - chr5:177238446 64.4 16410 254.7
23:49:11.121 INFO ProgressMeter - chr5:177512990 64.6 16460 254.7
23:49:21.588 INFO ProgressMeter - chr5:180620678 64.8 16520 255.0
23:49:32.996 INFO ProgressMeter - chr6:20411963 65.0 16580 255.2
23:49:43.523 INFO ProgressMeter - chr6:20481204 65.2 16630 255.2
23:49:53.781 INFO ProgressMeter - chr6:26045573 65.3 16680 255.3
23:50:05.419 INFO ProgressMeter - chr6:27890680 65.5 16730 255.4
23:50:15.477 INFO ProgressMeter - chr6:30704276 65.7 16760 255.2
23:50:28.556 INFO ProgressMeter - chr6:30713646 65.9 16800 254.9
23:50:39.677 INFO ProgressMeter - chr6:32220127 66.1 16860 255.1
23:50:49.853 INFO ProgressMeter - chr6:33321717 66.3 16900 255.1
23:51:00.768 INFO ProgressMeter - chr6:41957078 66.4 16970 255.4
23:51:12.168 INFO ProgressMeter - chr6:93246843 66.6 17040 255.7
23:51:23.207 INFO ProgressMeter - chr6:106104952 66.8 17090 255.8
23:51:34.626 INFO ProgressMeter - chr6:112061184 67.0 17130 255.7
23:51:49.299 INFO ProgressMeter - chr6:117319342 67.2 17170 255.3
23:52:03.489 INFO ProgressMeter - chr6:117322781 67.5 17200 254.9
23:52:14.178 INFO ProgressMeter - chr6:117326127 67.7 17230 254.6
23:52:26.826 INFO ProgressMeter - chr6:117329675 67.9 17270 254.4
23:52:37.686 INFO ProgressMeter - chr6:117333183 68.1 17300 254.2
23:52:50.053 INFO ProgressMeter - chr6:117338697 68.3 17350 254.2
23:53:01.510 INFO ProgressMeter - chr6:117360340 68.5 17390 254.0
23:53:13.148 INFO ProgressMeter - chr6:135198906 68.6 17450 254.2
23:53:26.054 INFO ProgressMeter - chr6:135205500 68.9 17480 253.8
23:53:37.930 INFO ProgressMeter - chr6:135209638 69.1 17510 253.6
23:53:53.850 INFO ProgressMeter - chr6:135212044 69.3 17530 252.9
23:54:05.914 INFO ProgressMeter - chr6:135215664 69.5 17560 252.6
23:54:16.055 INFO ProgressMeter - chr6:137204388 69.7 17590 252.4
23:54:27.852 INFO ProgressMeter - chr6:149683014 69.9 17640 252.4
23:54:39.130 INFO ProgressMeter - chr6:151804265 70.1 17680 252.3
23:54:50.273 INFO ProgressMeter - chr6:152041970 70.3 17720 252.2
23:55:02.490 INFO ProgressMeter - chr6:157148622 70.5 17770 252.2
23:55:16.066 INFO ProgressMeter - chr6:161049234 70.7 17820 252.1
23:55:26.588 INFO ProgressMeter - chr6:161350097 70.9 17870 252.2
23:55:37.463 INFO ProgressMeter - chr7:2923224 71.1 17930 252.4
23:55:49.502 INFO ProgressMeter - chr7:13892320 71.3 17990 252.5
23:56:00.027 INFO ProgressMeter - chr7:13895480 71.4 18020 252.3
23:56:14.216 INFO ProgressMeter - chr7:13909607 71.7 18050 251.9
23:56:26.396 INFO ProgressMeter - chr7:13934399 71.9 18080 251.6
23:56:38.484 INFO ProgressMeter - chr7:13938976 72.1 18120 251.4
23:56:50.578 INFO ProgressMeter - chr7:13943420 72.3 18160 251.3
23:57:01.493 INFO ProgressMeter - chr7:13945923 72.5 18180 250.9
23:57:12.370 INFO ProgressMeter - chr7:13948841 72.6 18210 250.7
23:57:25.049 INFO ProgressMeter - chr7:13951329 72.8 18230 250.3
23:57:37.185 INFO ProgressMeter - chr7:13953733 73.0 18250 249.8
23:57:47.227 INFO ProgressMeter - chr7:13958103 73.2 18280 249.7
23:58:00.741 INFO ProgressMeter - chr7:13962063 73.4 18320 249.5
23:58:13.391 INFO ProgressMeter - chr7:13965141 73.7 18340 249.0
23:58:24.950 INFO ProgressMeter - chr7:13969816 73.8 18380 248.9
23:58:36.636 INFO ProgressMeter - chr7:13973141 74.0 18410 248.7
23:58:55.113 INFO ProgressMeter - chr7:13976215 74.3 18440 248.0
23:59:05.864 INFO ProgressMeter - chr7:13980279 74.5 18470 247.8
23:59:16.635 INFO ProgressMeter - chr7:13983302 74.7 18500 247.6
23:59:34.272 INFO ProgressMeter - chr7:13988530 75.0 18540 247.2
23:59:46.167 INFO ProgressMeter - chr7:55069031 75.2 18590 247.2
23:59:57.912 INFO ProgressMeter - chr7:55156759 75.4 18630 247.1
00:00:10.780 INFO ProgressMeter - chr7:55167697 75.6 18660 246.8
00:00:20.941 INFO ProgressMeter - chr7:55170948 75.8 18690 246.6
00:00:31.556 INFO ProgressMeter - chr7:55177233 76.0 18720 246.5
00:00:43.420 INFO ProgressMeter - chr7:55180427 76.2 18750 246.2
00:00:55.183 INFO ProgressMeter - chr7:55201734 76.3 18790 246.1
00:01:05.651 INFO ProgressMeter - chr7:78256497 76.5 18830 246.1
00:01:16.678 INFO ProgressMeter - chr7:86786332 76.7 18880 246.1
00:01:27.525 INFO ProgressMeter - chr7:92661796 76.9 18920 246.1
00:01:38.491 INFO ProgressMeter - chr7:101916094 77.1 18970 246.1
00:01:50.731 INFO ProgressMeter - chr7:102227346 77.3 19010 246.0
00:02:04.173 INFO ProgressMeter - chr7:106868582 77.5 19050 245.8
00:02:15.324 INFO ProgressMeter - chr7:116700070 77.7 19080 245.6
00:02:28.563 INFO ProgressMeter - chr7:116771809 77.9 19120 245.4
00:02:39.367 INFO ProgressMeter - chr7:129206148 78.1 19160 245.4
00:02:50.900 INFO ProgressMeter - chr7:140777989 78.3 19200 245.3
00:03:01.758 INFO ProgressMeter - chr7:140791362 78.5 19230 245.1
00:03:11.818 INFO ProgressMeter - chr7:140797644 78.6 19260 245.0
00:03:22.585 INFO ProgressMeter - chr7:142942432 78.8 19310 245.0
00:03:34.193 INFO ProgressMeter - chr7:151467131 79.0 19370 245.2
00:03:46.868 INFO ProgressMeter - chr7:152162382 79.2 19420 245.2
00:03:58.294 INFO ProgressMeter - chr7:152177905 79.4 19450 245.0
00:04:08.554 INFO ProgressMeter - chr7:152194032 79.6 19480 244.8
00:04:19.688 INFO ProgressMeter - chr7:152435624 79.8 19540 245.0
00:04:29.935 INFO ProgressMeter - chr8:26293214 79.9 19590 245.1
00:04:40.026 INFO ProgressMeter - chr8:32548778 80.1 19650 245.3
00:04:51.093 INFO ProgressMeter - chr8:32728350 80.3 19680 245.1
00:05:01.842 INFO ProgressMeter - chr8:37697144 80.5 19720 245.1
00:05:13.987 INFO ProgressMeter - chr8:37841880 80.7 19770 245.1
00:05:26.523 INFO ProgressMeter - chr8:38437079 80.9 19820 245.1
00:05:37.494 INFO ProgressMeter - chr8:41933832 81.1 19860 245.0
00:05:47.728 INFO ProgressMeter - chr8:41987454 81.2 19900 245.0
00:05:58.723 INFO ProgressMeter - chr8:47826812 81.4 19960 245.2
00:06:09.113 INFO ProgressMeter - chr8:47900371 81.6 20020 245.4
00:06:20.075 INFO ProgressMeter - chr8:55966841 81.8 20090 245.7
00:06:30.601 INFO ProgressMeter - chr8:68134260 81.9 20150 245.9
00:06:42.715 INFO ProgressMeter - chr8:92005173 82.1 20220 246.2
00:06:56.505 INFO ProgressMeter - chr8:127733891 82.4 20270 246.1
00:07:07.685 INFO ProgressMeter - chr8:144511540 82.6 20330 246.3
00:07:17.770 INFO ProgressMeter - chr9:5022090 82.7 20380 246.4
00:07:29.146 INFO ProgressMeter - chr9:5549333 82.9 20450 246.6
00:07:41.388 INFO ProgressMeter - chr9:8521441 83.1 20520 246.9
00:07:51.584 INFO ProgressMeter - chr9:21968227 83.3 20560 246.9
00:08:01.877 INFO ProgressMeter - chr9:35078635 83.5 20610 246.9
00:08:12.947 INFO ProgressMeter - chr9:83978174 83.6 20670 247.1
00:08:27.477 INFO ProgressMeter - chr9:84743392 83.9 20710 246.9
00:08:38.611 INFO ProgressMeter - chr9:84812108 84.1 20740 246.7
00:08:48.630 INFO ProgressMeter - chr9:84814003 84.2 20760 246.4
00:09:00.718 INFO ProgressMeter - chr9:84861760 84.4 20780 246.1
00:09:17.366 INFO ProgressMeter - chr9:84865679 84.7 20810 245.6
00:09:30.543 INFO ProgressMeter - chr9:84874488 84.9 20850 245.5
00:09:41.524 INFO ProgressMeter - chr9:84955281 85.1 20880 245.3
00:09:53.715 INFO ProgressMeter - chr9:85023629 85.3 20910 245.1
00:10:08.310 INFO ProgressMeter - chr9:85026970 85.6 20940 244.7
00:10:19.053 INFO ProgressMeter - chr9:95449067 85.7 21000 244.9
00:10:30.448 INFO ProgressMeter - chr9:99128853 85.9 21060 245.1
00:10:42.845 INFO ProgressMeter - chr9:130872858 86.1 21130 245.3
00:10:54.965 INFO ProgressMeter - chr9:132896507 86.3 21170 245.2
00:11:05.384 INFO ProgressMeter - chr9:136496129 86.5 21210 245.2
00:11:15.934 INFO ProgressMeter - chr9:136505308 86.7 21240 245.0
00:11:27.602 INFO ProgressMeter - chr9:136898739 86.9 21310 245.3
00:11:39.921 INFO ProgressMeter - chrX:40062945 87.1 21380 245.5
00:11:49.992 INFO ProgressMeter - chrX:40074605 87.3 21410 245.4
00:12:02.014 INFO ProgressMeter - chrX:47173126 87.5 21480 245.6
00:12:12.647 INFO ProgressMeter - chrX:47571321 87.6 21530 245.7
00:12:23.960 INFO ProgressMeter - chrX:49034780 87.8 21570 245.6
00:12:38.174 INFO ProgressMeter - chrX:49037747 88.1 21600 245.3
00:12:48.748 INFO ProgressMeter - chrX:53195914 88.2 21640 245.2
00:12:58.760 INFO ProgressMeter - chrX:53382507 88.4 21690 245.3
00:13:09.685 INFO ProgressMeter - chrX:53413211 88.6 21730 245.3
00:13:22.014 INFO ProgressMeter - chrX:64193028 88.8 21770 245.2
00:13:32.145 INFO ProgressMeter - chrX:67545899 89.0 21790 244.9
00:13:42.339 INFO ProgressMeter - chrX:67658808 89.1 21840 245.0
00:13:52.383 INFO ProgressMeter - chrX:71125349 89.3 21890 245.1
00:14:03.801 INFO ProgressMeter - chrX:71140633 89.5 21940 245.2
00:14:14.117 INFO ProgressMeter - chrX:71397359 89.7 21990 245.3
00:14:24.291 INFO ProgressMeter - chrX:77558762 89.8 22040 245.3
00:14:36.007 INFO ProgressMeter - chrX:77682883 90.0 22090 245.4
00:14:46.138 INFO ProgressMeter - chrX:101362688 90.2 22140 245.5
00:14:56.869 INFO ProgressMeter - chrX:123907151 90.4 22200 245.6
00:15:07.650 INFO ProgressMeter - chrX:124371349 90.6 22260 245.8
00:15:19.028 INFO ProgressMeter - chrX:130025068 90.7 22300 245.7
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
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 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