Using GATK jar /data/common/tools/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-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 -jar /data/common/tools/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar VariantEval -R Homo_sapiens.GRCh37.dna.primary_assembly.fa -O all.vcf.eval.grp --eval all.vcf.gz --dbsnp dbsnp_138.b37.vcf log4j:WARN No appenders could be found for logger (org.reflections.Reflections). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. 14:15:02.978 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data/common/tools/GATK/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Nov 13, 2019 2:15:04 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 14:15:04.934 INFO VariantEval - ------------------------------------------------------------ 14:15:04.935 INFO VariantEval - The Genome Analysis Toolkit (GATK) v4.1.2.0 14:15:04.935 INFO VariantEval - For support and documentation go to https://software.broadinstitute.org/gatk/ 14:15:04.936 INFO VariantEval - Executing as paalmbj@loki.ous.nsc.local on Linux v3.10.0-1062.4.1.el7.x86_64 amd64 14:15:04.938 INFO VariantEval - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_121-b13 14:15:04.938 INFO VariantEval - Start Date/Time: November 13, 2019 2:15:02 PM CET 14:15:04.939 INFO VariantEval - ------------------------------------------------------------ 14:15:04.939 INFO VariantEval - ------------------------------------------------------------ 14:15:04.940 INFO VariantEval - HTSJDK Version: 2.19.0 14:15:04.940 INFO VariantEval - Picard Version: 2.19.0 14:15:04.940 INFO VariantEval - HTSJDK Defaults.COMPRESSION_LEVEL : 2 14:15:04.941 INFO VariantEval - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 14:15:04.941 INFO VariantEval - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 14:15:04.941 INFO VariantEval - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 14:15:04.941 INFO VariantEval - Deflater: IntelDeflater 14:15:04.942 INFO VariantEval - Inflater: IntelInflater 14:15:04.942 INFO VariantEval - GCS max retries/reopens: 20 14:15:04.942 INFO VariantEval - Requester pays: disabled 14:15:04.943 WARN VariantEval -  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: VariantEval is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 14:15:04.943 INFO VariantEval - Initializing engine 14:15:05.639 INFO FeatureManager - Using codec VCFCodec to read file file:///data/runScratch.boston/analysis/projects/Bermejo-WGS1-2019-09-02/work/53/9417836b2c6edb4a99d25303dc23d5/all.vcf.gz 14:15:05.995 INFO FeatureManager - Using codec VCFCodec to read file file:///data/runScratch.boston/analysis/projects/Bermejo-WGS1-2019-09-02/work/53/9417836b2c6edb4a99d25303dc23d5/dbsnp_138.b37.vcf 14:15:07.236 INFO VariantEval - Done initializing engine 14:15:07.247 INFO VariantEval - Creating 3 combinatorial stratification states 14:15:07.250 INFO ProgressMeter - Starting traversal 14:15:07.251 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 14:15:17.266 INFO ProgressMeter - 1:2629136 0.2 73000 437518.7 14:15:27.303 INFO ProgressMeter - 1:9305365 0.3 262000 784000.8 14:15:37.323 INFO ProgressMeter - 1:16553570 0.5 450000 897845.2 14:15:47.344 INFO ProgressMeter - 1:23510592 0.7 649000 971266.1 14:15:57.376 INFO ProgressMeter - 1:32146575 0.8 862000 1031841.0 14:16:07.397 INFO ProgressMeter - 1:42547525 1.0 1114000 1111314.3 14:16:17.397 INFO ProgressMeter - 1:54282318 1.2 1383000 1182961.3 14:16:27.409 INFO ProgressMeter - 1:64121569 1.3 1626000 1217111.4 14:16:37.622 INFO ProgressMeter - 1:74369915 1.5 1862000 1236251.0 14:16:47.668 INFO ProgressMeter - 1:83278744 1.7 2079000 1242219.9 14:16:57.682 INFO ProgressMeter - 1:93525648 1.8 2320000 1260515.6 14:17:07.728 INFO ProgressMeter - 1:102619774 2.0 2534000 1261994.1 14:17:17.787 INFO ProgressMeter - 1:113241552 2.2 2793000 1283783.8 14:17:27.863 INFO ProgressMeter - 1:142641435 2.3 3006000 1282678.6 14:17:37.874 INFO ProgressMeter - 1:150830779 2.5 3188000 1269925.6 14:17:47.883 INFO ProgressMeter - 1:160361971 2.7 3433000 1282309.9 14:17:57.887 INFO ProgressMeter - 1:169188092 2.8 3661000 1287309.2 14:18:07.922 INFO ProgressMeter - 1:180060703 3.0 3917000 1300824.7 14:18:17.973 INFO ProgressMeter - 1:189968994 3.2 4160000 1308711.1 14:18:28.024 INFO ProgressMeter - 1:200206138 3.3 4404000 1316119.8 14:18:38.070 INFO ProgressMeter - 1:208905613 3.5 4648000 1322840.9 14:18:48.114 INFO ProgressMeter - 1:218513393 3.7 4883000 1326529.7 14:18:58.116 INFO ProgressMeter - 1:228630660 3.8 5126000 1332207.1 14:19:08.136 INFO ProgressMeter - 1:236455439 4.0 5329000 1327360.9 14:19:18.179 INFO ProgressMeter - 1:243214701 4.2 5519000 1319661.4 14:19:28.233 INFO ProgressMeter - 10:1979527 4.3 5695000 1309285.7 14:19:38.305 INFO ProgressMeter - 10:12231893 4.5 5746000 1271923.7 14:19:48.367 INFO ProgressMeter - 10:24673310 4.7 5801000 1238136.6 14:19:58.482 INFO ProgressMeter - 10:35309094 4.9 5851000 1205439.0 14:20:08.644 INFO ProgressMeter - 10:45464100 5.0 5910000 1176536.9 14:20:18.805 INFO ProgressMeter - 10:60265256 5.2 5967000 1149142.7 14:20:28.811 INFO ProgressMeter - 10:72129976 5.4 6016000 1122527.7 14:20:38.957 INFO ProgressMeter - 10:86026477 5.5 6069000 1097779.4 14:20:48.972 INFO ProgressMeter - 10:100113281 5.7 6122000 1074915.1 14:20:58.980 INFO ProgressMeter - 10:114519462 5.9 6176000 1053541.4 14:21:09.100 INFO ProgressMeter - 10:126678092 6.0 6227000 1032595.8 14:21:19.137 INFO ProgressMeter - 11:1845383 6.2 6280000 1013213.7 14:21:29.277 INFO ProgressMeter - 11:12326089 6.4 6334000 994801.4 14:21:39.405 INFO ProgressMeter - 11:24211321 6.5 6386000 977067.6 14:21:49.605 INFO ProgressMeter - 11:36510026 6.7 6438000 960052.5 14:21:59.619 INFO ProgressMeter - 11:48379824 6.9 6488000 944013.5 14:22:09.620 INFO ProgressMeter - 11:61938444 7.0 6541000 929191.9 14:22:19.688 INFO ProgressMeter - 11:75657015 7.2 6595000 915046.6 14:22:29.723 INFO ProgressMeter - 11:89859797 7.4 6651000 901887.6 14:22:39.775 INFO ProgressMeter - 11:102212209 7.5 6704000 888883.0 14:22:49.843 INFO ProgressMeter - 11:116277011 7.7 6757000 876409.4 14:23:00.007 INFO ProgressMeter - 11:127959131 7.9 6804000 863532.1 14:23:10.244 INFO ProgressMeter - 12:5748656 8.0 6857000 851815.4 14:23:20.432 INFO ProgressMeter - 12:17364274 8.2 6910000 840665.0 14:23:30.589 INFO ProgressMeter - 12:30945379 8.4 6967000 830495.6 14:23:40.717 INFO ProgressMeter - 12:43171109 8.6 7019000 820190.6 14:23:50.745 INFO ProgressMeter - 12:57057542 8.7 7072000 810553.7 14:24:00.819 INFO ProgressMeter - 12:69996714 8.9 7121000 800760.2 14:24:10.957 INFO ProgressMeter - 12:84993595 9.1 7176000 791898.6 14:24:21.133 INFO ProgressMeter - 12:98479738 9.2 7227000 782874.3 14:24:31.241 INFO ProgressMeter - 12:112360168 9.4 7280000 774481.8 14:24:41.285 INFO ProgressMeter - 12:125070648 9.6 7334000 766574.8 14:24:51.296 INFO ProgressMeter - 13:19649665 9.7 7384000 758571.7 14:25:01.421 INFO ProgressMeter - 13:30636643 9.9 7437000 750997.2 14:25:11.540 INFO ProgressMeter - 13:44052241 10.1 7491000 743783.2 14:25:21.698 INFO ProgressMeter - 13:59216691 10.2 7544000 736662.4 14:25:31.742 INFO ProgressMeter - 13:73349527 10.4 7600000 730195.8 14:25:41.772 INFO ProgressMeter - 13:87234412 10.6 7656000 723947.7 14:25:51.808 INFO ProgressMeter - 13:100737083 10.7 7708000 717517.2 14:26:01.916 INFO ProgressMeter - 13:111978210 10.9 7759000 711111.8 14:26:12.035 INFO ProgressMeter - 14:26292160 11.1 7818000 705612.7 14:26:22.073 INFO ProgressMeter - 14:41003964 11.2 7874000 700095.7 14:26:32.319 INFO ProgressMeter - 14:54334390 11.4 7927000 694267.9 14:26:42.540 INFO ProgressMeter - 14:69166937 11.6 7982000 688807.1 14:26:52.630 INFO ProgressMeter - 14:81923911 11.8 8032000 683208.2 14:27:02.637 INFO ProgressMeter - 14:94214284 11.9 8080000 677676.1 14:27:12.865 INFO ProgressMeter - 14:106195479 12.1 8134000 672590.9 14:27:23.011 INFO ProgressMeter - 15:25996863 12.3 8192000 668044.8 14:27:33.088 INFO ProgressMeter - 15:37936978 12.4 8243000 663120.8 14:27:43.509 INFO ProgressMeter - 15:50907347 12.6 8292000 657870.7 14:27:53.690 INFO ProgressMeter - 15:61761440 12.8 8342000 653047.0 14:28:03.780 INFO ProgressMeter - 15:74760321 12.9 8389000 648193.0 14:28:13.855 INFO ProgressMeter - 15:87019916 13.1 8435000 643398.7 14:28:23.895 INFO ProgressMeter - 15:97329766 13.3 8478000 638528.6 14:28:34.043 INFO ProgressMeter - 16:4384171 13.4 8525000 633992.4 14:28:44.044 INFO ProgressMeter - 16:13054533 13.6 8577000 630049.5 14:28:54.173 INFO ProgressMeter - 16:25471755 13.8 8627000 625959.9 14:29:04.617 INFO ProgressMeter - 16:33945496 14.0 8685000 622309.3 14:29:14.659 INFO ProgressMeter - 16:54347943 14.1 8737000 618616.6 14:29:24.676 INFO ProgressMeter - 16:67076891 14.3 8789000 615027.6 14:29:34.922 INFO ProgressMeter - 16:78939331 14.5 8841000 611361.5 14:29:45.046 INFO ProgressMeter - 16:86399922 14.6 8887000 607453.9 14:29:55.222 INFO ProgressMeter - 17:5324236 14.8 8938000 603939.3 14:30:05.349 INFO ProgressMeter - 17:15190834 15.0 8986000 600336.0 14:30:15.405 INFO ProgressMeter - 17:27055440 15.1 9036000 596991.9 14:30:25.485 INFO ProgressMeter - 17:38430929 15.3 9078000 593182.8 14:30:35.539 INFO ProgressMeter - 17:50184479 15.5 9125000 589796.0 14:30:45.565 INFO ProgressMeter - 17:63507997 15.6 9172000 586499.4 14:30:55.793 INFO ProgressMeter - 17:73318368 15.8 9214000 582832.6 14:31:05.906 INFO ProgressMeter - 18:673995 16.0 9261000 579625.2 14:31:16.038 INFO ProgressMeter - 18:10294595 16.1 9305000 576288.3 14:31:26.197 INFO ProgressMeter - 18:22287503 16.3 9352000 573188.5 14:31:36.293 INFO ProgressMeter - 18:36208272 16.5 9398000 570128.0 14:31:46.436 INFO ProgressMeter - 18:48727135 16.7 9443000 567042.7 14:31:56.475 INFO ProgressMeter - 18:59716092 16.8 9488000 564077.5 14:32:06.540 INFO ProgressMeter - 18:70196128 17.0 9535000 561274.1 14:32:16.604 INFO ProgressMeter - 19:927357 17.2 9580000 558409.6 14:32:26.700 INFO ProgressMeter - 19:9890030 17.3 9632000 555987.4 14:32:36.785 INFO ProgressMeter - 19:19755946 17.5 9681000 553446.2 14:32:46.824 INFO ProgressMeter - 19:30369485 17.7 9729000 550920.6 14:32:57.018 INFO ProgressMeter - 19:39969095 17.8 9769000 547913.7 14:33:07.271 INFO ProgressMeter - 19:50125854 18.0 9816000 545323.7 14:33:17.361 INFO ProgressMeter - 19:57782851 18.2 9861000 542753.1 14:33:27.373 INFO ProgressMeter - 2:5637805 18.3 10027000 546867.1 14:33:37.410 INFO ProgressMeter - 2:13522431 18.5 10235000 553164.5 14:33:47.413 INFO ProgressMeter - 2:22040398 18.7 10444000 559419.6 14:33:57.418 INFO ProgressMeter - 2:30115895 18.8 10637000 564713.5 14:34:07.460 INFO ProgressMeter - 2:37473179 19.0 10842000 570527.5 14:34:17.490 INFO ProgressMeter - 2:44343974 19.2 11045000 576141.6 14:34:27.517 INFO ProgressMeter - 2:50968624 19.3 11230000 580729.4 14:34:37.552 INFO ProgressMeter - 2:58625676 19.5 11443000 586670.1 14:34:47.562 INFO ProgressMeter - 2:67768777 19.7 11658000 592624.0 14:34:57.579 INFO ProgressMeter - 2:75171684 19.8 11841000 596861.2 14:35:07.619 INFO ProgressMeter - 2:83378575 20.0 12053000 602465.2 14:35:17.635 INFO ProgressMeter - 2:92145621 20.2 12237000 606601.4 14:35:27.634 INFO ProgressMeter - 2:101620041 20.3 12400000 609644.7 14:35:37.661 INFO ProgressMeter - 2:111154950 20.5 12619000 615356.4 14:35:47.682 INFO ProgressMeter - 2:121649620 20.7 12862000 622142.6 14:35:57.689 INFO ProgressMeter - 2:129996988 20.8 13101000 628628.2 14:36:07.688 INFO ProgressMeter - 2:137024541 21.0 13295000 632875.7 14:36:17.698 INFO ProgressMeter - 2:145710251 21.2 13506000 637854.7 14:36:27.753 INFO ProgressMeter - 2:155114377 21.3 13716000 642685.9 14:36:37.788 INFO ProgressMeter - 2:166512972 21.5 13968000 649405.6 14:36:47.827 INFO ProgressMeter - 2:174530351 21.7 14174000 653895.4 14:36:57.840 INFO ProgressMeter - 2:183737913 21.8 14391000 658834.1 14:37:07.894 INFO ProgressMeter - 2:192849419 22.0 14599000 663268.3 14:37:17.925 INFO ProgressMeter - 2:202378254 22.2 14805000 667556.9 14:37:27.982 INFO ProgressMeter - 2:211565999 22.3 15017000 672036.4 14:37:38.010 INFO ProgressMeter - 2:219373618 22.5 15215000 675842.7 14:37:48.030 INFO ProgressMeter - 2:226302875 22.7 15390000 678583.4 14:37:58.083 INFO ProgressMeter - 2:233764516 22.8 15583000 682053.4 14:38:08.117 INFO ProgressMeter - 2:241594381 23.0 15804000 686700.0 14:38:18.178 INFO ProgressMeter - 20:9298492 23.2 15892000 685528.9 14:38:28.310 INFO ProgressMeter - 20:22236931 23.4 15944000 682798.3 14:38:38.409 INFO ProgressMeter - 20:32092456 23.5 15996000 680122.8 14:38:48.556 INFO ProgressMeter - 20:45979197 23.7 16048000 677461.9 14:38:58.711 INFO ProgressMeter - 20:57980957 23.9 16102000 674919.8 14:39:08.860 INFO ProgressMeter - 21:10717087 24.0 16149000 672124.0 14:39:18.938 INFO ProgressMeter - 21:20529616 24.2 16200000 669566.3 14:39:28.983 INFO ProgressMeter - 21:32644046 24.4 16252000 667099.5 14:39:39.031 INFO ProgressMeter - 21:44174275 24.5 16301000 664542.3 14:39:49.050 INFO ProgressMeter - 22:20655932 24.7 16351000 662074.0 14:39:59.262 INFO ProgressMeter - 22:30777881 24.9 16400000 659513.0 14:40:09.381 INFO ProgressMeter - 22:40043812 25.0 16441000 656707.5 14:40:19.573 INFO ProgressMeter - 22:50191572 25.2 16490000 654225.8 14:40:29.597 INFO ProgressMeter - 3:5714783 25.4 16681000 657446.2 14:40:39.623 INFO ProgressMeter - 3:12186081 25.5 16866000 660388.4 14:40:49.658 INFO ProgressMeter - 3:20479339 25.7 17073000 664144.2 14:40:59.683 INFO ProgressMeter - 3:28083137 25.9 17281000 667894.4 14:41:09.700 INFO ProgressMeter - 3:36006463 26.0 17477000 671140.9 14:41:19.769 INFO ProgressMeter - 3:45284666 26.2 17699000 675312.3 14:41:29.799 INFO ProgressMeter - 3:54447023 26.4 17911000 679069.9 14:41:39.822 INFO ProgressMeter - 3:61740029 26.5 18104000 682067.4 14:41:49.869 INFO ProgressMeter - 3:69433569 26.7 18307000 685391.5 14:41:59.954 INFO ProgressMeter - 3:76102716 26.9 18499000 688248.7 14:42:09.975 INFO ProgressMeter - 3:84513752 27.0 18699000 691393.0 14:42:19.993 INFO ProgressMeter - 3:95329215 27.2 18904000 694684.6 14:42:30.172 INFO ProgressMeter - 3:103473492 27.4 19108000 697830.7 14:42:40.190 INFO ProgressMeter - 3:111141151 27.5 19295000 700389.7 14:42:50.206 INFO ProgressMeter - 3:118955003 27.7 19482000 702917.8 14:43:00.218 INFO ProgressMeter - 3:127029648 27.9 19688000 706099.2 14:43:10.238 INFO ProgressMeter - 3:135746645 28.0 19905000 709631.6 14:43:20.272 INFO ProgressMeter - 3:145442540 28.2 20134000 713541.1 14:43:30.325 INFO ProgressMeter - 3:155552487 28.4 20379000 717961.0 14:43:40.352 INFO ProgressMeter - 3:166274232 28.6 20637000 722794.5 14:43:50.401 INFO ProgressMeter - 3:175951705 28.7 20871000 726727.2 14:44:00.442 INFO ProgressMeter - 3:185286346 28.9 21094000 730237.3 14:44:10.472 INFO ProgressMeter - 3:192906558 29.1 21297000 733022.8 14:44:20.486 INFO ProgressMeter - 4:2863714 29.2 21537000 737048.9 14:44:30.514 INFO ProgressMeter - 4:9138282 29.4 21748000 740037.5 14:44:40.522 INFO ProgressMeter - 4:15682239 29.6 21941000 742391.2 14:44:50.589 INFO ProgressMeter - 4:23638002 29.7 22142000 744963.0 14:45:00.592 INFO ProgressMeter - 4:31870290 29.9 22355000 747934.0 14:45:10.620 INFO ProgressMeter - 4:38735901 30.1 22539000 749896.9 14:45:20.643 INFO ProgressMeter - 4:46216605 30.2 22735000 752236.7 14:45:30.693 INFO ProgressMeter - 4:54589591 30.4 22905000 753684.9 14:45:40.696 INFO ProgressMeter - 4:61515225 30.6 23096000 755823.5 14:45:50.712 INFO ProgressMeter - 4:68936733 30.7 23292000 758096.2 14:46:00.714 INFO ProgressMeter - 4:76900137 30.9 23500000 760738.6 14:46:10.718 INFO ProgressMeter - 4:85789825 31.1 23714000 763544.9 14:46:20.770 INFO ProgressMeter - 4:93928328 31.2 23906000 765597.1 14:46:30.773 INFO ProgressMeter - 4:102689501 31.4 24111000 768061.5 14:46:40.808 INFO ProgressMeter - 4:112098845 31.6 24328000 770867.1 14:46:50.874 INFO ProgressMeter - 4:120357250 31.7 24526000 773031.6 14:47:00.884 INFO ProgressMeter - 4:128814543 31.9 24729000 775353.2 14:47:10.908 INFO ProgressMeter - 4:136763839 32.1 24929000 777550.7 14:47:20.949 INFO ProgressMeter - 4:144757945 32.2 25123000 779532.7 14:47:30.950 INFO ProgressMeter - 4:153584166 32.4 25322000 781664.6 14:47:40.952 INFO ProgressMeter - 4:160893766 32.6 25499000 783098.7 14:47:50.962 INFO ProgressMeter - 4:168304315 32.7 25693000 785034.5 14:48:00.963 INFO ProgressMeter - 4:177359186 32.9 25914000 787774.9 14:48:10.983 INFO ProgressMeter - 4:183785498 33.1 26091000 789149.3 14:48:21.014 INFO ProgressMeter - 4:190130791 33.2 26282000 790926.9 14:48:31.043 INFO ProgressMeter - 5:3963020 33.4 26467000 792507.4 14:48:41.096 INFO ProgressMeter - 5:11149437 33.6 26664000 794421.0 14:48:51.105 INFO ProgressMeter - 5:18752816 33.7 26858000 796243.6 14:49:01.112 INFO ProgressMeter - 5:26705371 33.9 27059000 798255.5 14:49:11.123 INFO ProgressMeter - 5:33821616 34.1 27248000 799893.9 14:49:21.135 INFO ProgressMeter - 5:41218620 34.2 27437000 801516.0 14:49:31.197 INFO ProgressMeter - 5:51908963 34.4 27652000 803858.2 14:49:41.263 INFO ProgressMeter - 5:59518569 34.6 27840000 805396.3 14:49:51.301 INFO ProgressMeter - 5:68648253 34.7 28051000 807591.4 14:50:01.319 INFO ProgressMeter - 5:78642355 34.9 28255000 809573.0 14:50:11.322 INFO ProgressMeter - 5:87514004 35.1 28463000 811655.5 14:50:21.375 INFO ProgressMeter - 5:97904138 35.2 28682000 814011.3 14:50:31.379 INFO ProgressMeter - 5:107030053 35.4 28902000 816391.9 14:50:41.396 INFO ProgressMeter - 5:114462236 35.6 29101000 818154.7 14:50:51.413 INFO ProgressMeter - 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9:115867814 48.3 45572000 943909.5 15:03:34.065 INFO ProgressMeter - 9:126084717 48.4 45820000 945777.7 15:03:44.086 INFO ProgressMeter - 9:134157685 48.6 46030000 946848.2 15:03:52.808 INFO VariantEval - Shutting down engine [November 13, 2019 3:03:52 PM CET] org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEval done. Elapsed time: 48.83 minutes. Runtime.totalMemory()=12447121408 java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:107) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:117) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205) at org.broadinstitute.hellbender.Main.main(Main.java:291)