Script started on Thu 27 Sep 2012 02:37:32 PM EDT INFO 14:37:36,800 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:37:36,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-9-gb90951c, Compiled 2012/09/19 21:18:53 INFO 14:37:36,803 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:37:36,803 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 14:37:36,804 HelpFormatter - Program Args: -T RealignerTargetCreator -R reference.fasta -I input.bam -o forIndelRealigner.interval_list --known reference_snps.vcf --validation_strictness LENIENT INFO 14:37:36,804 HelpFormatter - Date/Time: 2012/09/27 14:37:36 INFO 14:37:36,805 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:37:36,805 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:37:36,823 ArgumentTypeDescriptor - Dynamically determined type of reference_snps.vcf to be VCF INFO 14:37:36,828 GenomeAnalysisEngine - Strictness is LENIENT INFO 14:37:58,797 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:38:04,784 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 5.98 INFO 14:38:04,866 RMDTrackBuilder - Loading Tribble index from disk for file reference_snps.vcf INFO 14:38:14,398 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] INFO 14:38:14,401 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 14:38:44,326 TraversalEngine - chr1:3375785-3376092:214 1.44e+05 30.1 s 3.5 m 0.3% 3.1 h 3.0 h INFO 14:39:14,422 TraversalEngine - chr1:8845806-8846064:181 2.79e+05 60.2 s 3.6 m 0.5% 3.2 h 3.1 h INFO 14:39:44,574 TraversalEngine - chr1:11694909-11695148:53 4.06e+05 90.3 s 3.7 m 0.8% 3.3 h 3.2 h INFO 14:40:14,784 TraversalEngine - chr1:16127098-16135423:261 5.47e+05 2.0 m 3.7 m 1.0% 3.2 h 3.2 h INFO 14:40:44,868 TraversalEngine - chr1:19353924-19354231:104 6.81e+05 2.5 m 3.7 m 1.3% 3.2 h 3.2 h INFO 14:41:14,876 TraversalEngine - chr1:22079112-22079990:124 8.07e+05 3.0 m 3.7 m 1.5% 3.3 h 3.2 h INFO 14:41:45,024 TraversalEngine - chr1:26000046-26000313:17 9.38e+05 3.5 m 3.7 m 1.8% 3.3 h 3.2 h INFO 14:42:15,091 TraversalEngine - chr1:28431944-28432171:38 1.08e+06 4.0 m 3.7 m 2.0% 3.3 h 3.2 h INFO 14:42:45,179 TraversalEngine - chr1:32601708-32602519:654 1.21e+06 4.5 m 3.7 m 2.3% 3.3 h 3.2 h INFO 14:43:15,265 TraversalEngine - chr1:36335682-36337750:133 1.35e+06 5.0 m 3.7 m 2.6% 3.3 h 3.2 h INFO 14:43:45,462 TraversalEngine - chr1:40086170-40086431:153 1.49e+06 5.5 m 3.7 m 2.8% 3.2 h 3.2 h INFO 14:44:15,519 TraversalEngine - chr1:43836903-43837246:53 1.64e+06 6.0 m 3.7 m 3.1% 3.2 h 3.1 h INFO 14:44:45,671 TraversalEngine - chr1:46814759-46814988:127 1.78e+06 6.5 m 3.7 m 3.4% 3.2 h 3.1 h INFO 14:45:15,880 TraversalEngine - chr1:53277102-53277381:253 1.91e+06 7.0 m 3.7 m 3.6% 3.2 h 3.1 h INFO 14:45:46,007 TraversalEngine - chr1:60100969-60101212:86 2.02e+06 7.5 m 3.7 m 3.8% 3.3 h 3.1 h INFO 14:46:16,079 TraversalEngine - chr1:67196255-67196566:11 2.15e+06 8.0 m 3.7 m 4.1% 3.3 h 3.2 h INFO 14:46:46,298 TraversalEngine - chr1:77968058-77968286:81 2.27e+06 8.5 m 3.8 m 4.3% 3.3 h 3.2 h INFO 14:47:16,411 TraversalEngine - chr1:89070940-89071197:235 2.39e+06 9.0 m 3.8 m 4.5% 3.3 h 3.2 h INFO 14:47:46,504 TraversalEngine - chr1:94411938-94412968:156 2.52e+06 9.5 m 3.8 m 4.8% 3.3 h 3.2 h INFO 14:48:16,741 TraversalEngine - chr1:104038049-104038396:74 2.64e+06 10.0 m 3.8 m 5.0% 3.3 h 3.2 h INFO 14:48:46,855 TraversalEngine - chr1:110538649-110538991:297 2.77e+06 10.5 m 3.8 m 5.3% 3.3 h 3.2 h INFO 14:49:17,037 TraversalEngine - chr1:115017978-115018301:82 2.91e+06 11.0 m 3.8 m 5.5% 3.3 h 3.1 h INFO 14:49:47,073 TraversalEngine - chr1:120736896-120737066:140 3.04e+06 11.5 m 3.8 m 5.8% 3.3 h 3.1 h INFO 14:50:17,633 TraversalEngine - chr1:146860946-146861339:58 3.15e+06 12.1 m 3.8 m 6.0% 3.4 h 3.2 h INFO 14:50:47,742 TraversalEngine - chr1:149481463-149481742:172 3.27e+06 12.6 m 3.8 m 6.2% 3.4 h 3.2 h INFO 14:51:17,818 TraversalEngine - chr1:151928831-151929155:90 3.41e+06 13.1 m 3.8 m 6.5% 3.4 h 3.1 h INFO 14:51:47,897 TraversalEngine - chr1:153448725-153449260:337 3.54e+06 13.6 m 3.8 m 6.7% 3.4 h 3.1 h INFO 14:52:17,905 TraversalEngine - chr1:154972973-154973244:77 3.69e+06 14.1 m 3.8 m 7.0% 3.3 h 3.1 h INFO 14:52:48,027 TraversalEngine - chr1:158168151-158168417:133 3.82e+06 14.6 m 3.8 m 7.3% 3.3 h 3.1 h INFO 14:53:18,039 TraversalEngine - chr1:159986141-159986634:42 3.95e+06 15.1 m 3.8 m 7.5% 3.3 h 3.1 h INFO 14:53:48,115 TraversalEngine - chr1:167756307-167756601:196 4.07e+06 15.6 m 3.8 m 7.7% 3.4 h 3.1 h INFO 14:54:18,220 TraversalEngine - chr1:174225046-174225313:40 4.20e+06 16.1 m 3.8 m 8.0% 3.4 h 3.1 h INFO 14:54:48,383 TraversalEngine - chr1:181451136-181451421:221 4.33e+06 16.6 m 3.8 m 8.2% 3.4 h 3.1 h INFO 14:55:18,558 TraversalEngine - chr1:188517238-188517578:213 4.45e+06 17.1 m 3.8 m 8.5% 3.4 h 3.1 h INFO 14:55:48,763 TraversalEngine - chr1:199296943-199297294:291 4.58e+06 17.6 m 3.8 m 8.7% 3.4 h 3.1 h INFO 14:56:18,848 TraversalEngine - chr1:202087817-202088225:31 4.71e+06 18.1 m 3.8 m 8.9% 3.4 h 3.1 h INFO 14:56:49,098 TraversalEngine - chr1:205311081-205311293:128 4.84e+06 18.6 m 3.8 m 9.2% 3.4 h 3.1 h INFO 14:57:19,146 TraversalEngine - chr1:212626735-212626963:160 4.97e+06 19.1 m 3.8 m 9.4% 3.4 h 3.1 h INFO 14:57:49,198 TraversalEngine - chr1:222003289-222003522:31 5.11e+06 19.6 m 3.8 m 9.7% 3.4 h 3.0 h INFO 14:58:19,298 TraversalEngine - chr1:227751529-227751879:292 5.24e+06 20.1 m 3.8 m 9.9% 3.4 h 3.0 h INFO 14:58:49,319 TraversalEngine - chr1:234450680-234450963:86 5.37e+06 20.6 m 3.8 m 10.2% 3.4 h 3.0 h INFO 14:59:19,359 TraversalEngine - chr1:245119816-245120059:8 5.49e+06 21.1 m 3.8 m 10.4% 3.4 h 3.0 h INFO 14:59:49,396 TraversalEngine - chr2:10137409-10137876:322 5.64e+06 21.6 m 3.8 m 10.7% 3.4 h 3.0 h INFO 15:00:19,428 TraversalEngine - chr2:21080571-21081127:169 5.77e+06 22.1 m 3.8 m 11.0% 3.4 h 3.0 h INFO 15:00:49,549 TraversalEngine - chr2:27281647-27281951:151 5.91e+06 22.6 m 3.8 m 11.2% 3.4 h 3.0 h INFO 15:01:19,710 TraversalEngine - chr2:29299637-29299973:97 6.04e+06 23.1 m 3.8 m 11.5% 3.4 h 3.0 h INFO 15:01:49,879 TraversalEngine - chr2:38666215-38666602:102 6.16e+06 23.6 m 3.8 m 11.7% 3.4 h 3.0 h INFO 15:02:19,930 TraversalEngine - chr2:47126883-47127149:142 6.29e+06 24.1 m 3.8 m 11.9% 3.4 h 3.0 h INFO 15:02:50,200 TraversalEngine - chr2:60849345-60849604:77 6.41e+06 24.6 m 3.8 m 12.2% 3.4 h 3.0 h INFO 15:03:20,388 TraversalEngine - chr2:69203578-69203797:194 6.54e+06 25.1 m 3.8 m 12.4% 3.4 h 2.9 h INFO 15:03:50,521 TraversalEngine - chr2:74302027-74302211:145 6.67e+06 25.6 m 3.8 m 12.7% 3.4 h 2.9 h INFO 15:04:20,602 TraversalEngine - chr2:86197089-86197307:14 6.81e+06 26.1 m 3.8 m 12.9% 3.4 h 2.9 h INFO 15:04:50,791 TraversalEngine - chr2:98098472-98098716:214 6.94e+06 26.6 m 3.8 m 13.2% 3.4 h 2.9 h INFO 15:05:21,040 TraversalEngine - chr2:108435212-108435429:57 7.08e+06 27.1 m 3.8 m 13.4% 3.4 h 2.9 h INFO 15:05:51,170 TraversalEngine - chr2:113548696-113548973:162 7.20e+06 27.6 m 3.8 m 13.7% 3.4 h 2.9 h INFO 15:06:21,373 TraversalEngine - chr2:128331997-128332219:134 7.32e+06 28.1 m 3.8 m 13.9% 3.4 h 2.9 h INFO 15:06:51,456 TraversalEngine - chr2:141010545-141010823:268 7.45e+06 28.6 m 3.8 m 14.1% 3.4 h 2.9 h INFO 15:07:21,649 TraversalEngine - chr2:160327562-160327825:149 7.59e+06 29.1 m 3.8 m 14.4% 3.4 h 2.9 h INFO 15:07:51,750 TraversalEngine - chr2:169334191-169334493:300 7.73e+06 29.6 m 3.8 m 14.7% 3.4 h 2.9 h INFO 15:08:21,943 TraversalEngine - chr2:173833962-173834186:75 7.85e+06 30.1 m 3.8 m 14.9% 3.4 h 2.9 h INFO 15:08:52,143 TraversalEngine - chr2:183537574-183537856:31 7.98e+06 30.6 m 3.8 m 15.2% 3.4 h 2.9 h INFO 15:09:22,143 TraversalEngine - chr2:191987413-191987715:223 8.10e+06 31.1 m 3.8 m 15.4% 3.4 h 2.9 h INFO 15:09:52,214 TraversalEngine - chr2:201581866-201582131:261 8.23e+06 31.6 m 3.8 m 15.6% 3.4 h 2.8 h INFO 15:10:22,300 TraversalEngine - chr2:207654107-207654308:166 8.35e+06 32.1 m 3.8 m 15.9% 3.4 h 2.8 h INFO 15:10:52,469 TraversalEngine - chr2:216694955-216695296:2 8.48e+06 32.6 m 3.8 m 16.1% 3.4 h 2.8 h INFO 15:11:22,585 TraversalEngine - chr2:219809963-219810388:121 8.62e+06 33.1 m 3.8 m 16.4% 3.4 h 2.8 h INFO 15:11:52,605 TraversalEngine - chr2:228464140-228464348:32 8.76e+06 33.6 m 3.8 m 16.6% 3.4 h 2.8 h INFO 15:12:22,775 TraversalEngine - chr2:234015197-234015455:185 8.89e+06 34.1 m 3.8 m 16.9% 3.4 h 2.8 h INFO 15:12:52,851 TraversalEngine - chr2:241700253-241700602:33 9.02e+06 34.6 m 3.8 m 17.1% 3.4 h 2.8 h INFO 15:13:22,963 TraversalEngine - chr3:9757388-9757700:27 9.16e+06 35.1 m 3.8 m 17.4% 3.4 h 2.8 h INFO 15:13:52,993 TraversalEngine - chr3:14155606-14155873:258 9.29e+06 35.6 m 3.8 m 17.6% 3.4 h 2.8 h INFO 15:14:23,113 TraversalEngine - chr3:30704805-30705082:38 9.41e+06 36.1 m 3.8 m 17.9% 3.4 h 2.8 h INFO 15:14:53,140 TraversalEngine - chr3:38330147-38330511:289 9.54e+06 36.6 m 3.8 m 18.1% 3.4 h 2.8 h INFO 15:15:23,151 TraversalEngine - chr3:44462996-44465310:1521 9.68e+06 37.1 m 3.8 m 18.4% 3.4 h 2.7 h INFO 15:15:53,224 TraversalEngine - chr3:47730834-47731059:100 9.83e+06 37.6 m 3.8 m 18.7% 3.4 h 2.7 h INFO 15:16:23,394 TraversalEngine - chr3:49429902-49430485:358 9.99e+06 38.2 m 3.8 m 19.0% 3.4 h 2.7 h INFO 15:16:53,488 TraversalEngine - chr3:52287182-52287492:291 1.02e+07 38.7 m 3.8 m 19.3% 3.3 h 2.7 h INFO 15:17:23,659 TraversalEngine - chr3:57255069-57255365:174 1.03e+07 39.2 m 3.8 m 19.6% 3.3 h 2.7 h INFO 15:17:53,789 TraversalEngine - chr3:67742494-67742785:45 1.04e+07 39.7 m 3.8 m 19.8% 3.3 h 2.7 h INFO 15:18:23,971 TraversalEngine - chr3:101946292-101946540:10 1.06e+07 40.2 m 3.8 m 20.1% 3.3 h 2.7 h INFO 15:18:54,144 TraversalEngine - chr3:113471378-113471689:278 1.07e+07 40.7 m 3.8 m 20.3% 3.3 h 2.7 h INFO 15:19:24,484 TraversalEngine - chr3:121891285-121891500:88 1.08e+07 41.2 m 3.8 m 20.6% 3.3 h 2.7 h INFO 15:19:54,640 TraversalEngine - chr3:125897596-125897867:101 1.10e+07 41.7 m 3.8 m 20.8% 3.3 h 2.6 h INFO 15:20:24,767 TraversalEngine - chr3:130721634-130721873:33 1.11e+07 42.2 m 3.8 m 21.1% 3.3 h 2.6 h INFO 15:20:54,775 TraversalEngine - chr3:137678746-137679019:230 1.12e+07 42.7 m 3.8 m 21.3% 3.3 h 2.6 h INFO 15:21:24,899 TraversalEngine - chr3:144583517-144583721:105 1.13e+07 43.2 m 3.8 m 21.5% 3.3 h 2.6 h INFO 15:21:54,971 TraversalEngine - chr3:158359274-158359533:137 1.15e+07 43.7 m 3.8 m 21.8% 3.3 h 2.6 h INFO 15:22:25,069 TraversalEngine - chr3:172874909-172875172:15 1.16e+07 44.2 m 3.8 m 22.1% 3.3 h 2.6 h INFO 15:22:55,089 TraversalEngine - chr3:185182858-185183564:685 1.17e+07 44.7 m 3.8 m 22.3% 3.3 h 2.6 h INFO 15:23:25,224 TraversalEngine - chr3:189606528-189606870:95 1.19e+07 45.2 m 3.8 m 22.6% 3.3 h 2.6 h INFO 15:23:55,319 TraversalEngine - chr3:198031564-198031910:61 1.20e+07 45.7 m 3.8 m 22.8% 3.3 h 2.6 h INFO 15:24:25,408 TraversalEngine - chr4:1954769-1955295:282 1.21e+07 46.2 m 3.8 m 23.1% 3.3 h 2.6 h INFO 15:24:55,423 TraversalEngine - chr4:6434330-6434549:197 1.23e+07 46.7 m 3.8 m 23.3% 3.3 h 2.6 h INFO 15:25:25,551 TraversalEngine - chr4:24734576-24735020:394 1.24e+07 47.2 m 3.8 m 23.6% 3.3 h 2.5 h INFO 15:25:55,565 TraversalEngine - chr4:41719537-41719779:157 1.26e+07 47.7 m 3.8 m 23.8% 3.3 h 2.5 h INFO 15:26:25,667 TraversalEngine - chr4:54819618-54819816:72 1.27e+07 48.2 m 3.8 m 24.1% 3.3 h 2.5 h INFO 15:26:55,706 TraversalEngine - chr4:69115999-69116872:411 1.28e+07 48.7 m 3.8 m 24.3% 3.3 h 2.5 h INFO 15:27:25,869 TraversalEngine - chr4:77000769-77001172:222 1.29e+07 49.2 m 3.8 m 24.5% 3.3 h 2.5 h INFO 15:27:55,903 TraversalEngine - chr4:85844440-85844696:119 1.31e+07 49.7 m 3.8 m 24.8% 3.3 h 2.5 h INFO 15:28:26,113 TraversalEngine - chr4:96359068-96359562:404 1.32e+07 50.2 m 3.8 m 25.0% 3.3 h 2.5 h INFO 15:28:56,261 TraversalEngine - chr4:107488057-107488373:50 1.33e+07 50.7 m 3.8 m 25.3% 3.3 h 2.5 h INFO 15:29:26,305 TraversalEngine - chr4:119898249-119898523:106 1.34e+07 51.2 m 3.8 m 25.5% 3.3 h 2.5 h INFO 15:29:56,454 TraversalEngine - chr4:129346958-129347217:250 1.36e+07 51.7 m 3.8 m 25.8% 3.3 h 2.5 h INFO 15:30:26,748 TraversalEngine - chr4:151380269-151380552:190 1.37e+07 52.2 m 3.8 m 26.0% 3.3 h 2.5 h INFO 15:30:56,941 TraversalEngine - chr4:159859707-159859963:219 1.38e+07 52.7 m 3.8 m 26.3% 3.3 h 2.5 h INFO 15:31:27,019 TraversalEngine - chr4:184668354-184669174:363 1.40e+07 53.2 m 3.8 m 26.5% 3.3 h 2.5 h INFO 15:31:57,030 TraversalEngine - chr5:1126673-1126991:10 1.41e+07 53.7 m 3.8 m 26.8% 3.3 h 2.4 h INFO 15:32:27,288 TraversalEngine - chr5:14196760-14197066:57 1.42e+07 54.2 m 3.8 m 27.0% 3.3 h 2.4 h INFO 15:32:57,350 TraversalEngine - chr5:35909264-35909582:100 1.44e+07 54.7 m 3.8 m 27.3% 3.3 h 2.4 h INFO 15:33:27,501 TraversalEngine - chr5:42724674-42724953:275 1.45e+07 55.2 m 3.8 m 27.5% 3.3 h 2.4 h INFO 15:33:57,645 TraversalEngine - chr5:56267175-56267410:93 1.46e+07 55.7 m 3.8 m 27.8% 3.3 h 2.4 h INFO 15:34:27,665 TraversalEngine - chr5:70319301-70319532:122 1.47e+07 56.2 m 3.8 m 28.0% 3.3 h 2.4 h INFO 15:34:57,854 TraversalEngine - chr5:77472648-77472974:75 1.49e+07 56.7 m 3.8 m 28.2% 3.3 h 2.4 h INFO 15:35:28,069 TraversalEngine - chr5:94645241-94646110:39 1.50e+07 57.2 m 3.8 m 28.5% 3.3 h 2.4 h INFO 15:35:58,175 TraversalEngine - chr5:110467309-110467591:170 1.51e+07 57.7 m 3.8 m 28.7% 3.3 h 2.4 h INFO 15:36:28,219 TraversalEngine - chr5:124107601-124108656:849 1.53e+07 58.2 m 3.8 m 29.0% 3.3 h 2.4 h INFO 15:36:58,496 TraversalEngine - chr5:132074475-132074723:117 1.54e+07 58.7 m 3.8 m 29.2% 3.4 h 2.4 h INFO 15:37:28,562 TraversalEngine - chr5:137749535-137750284:95 1.55e+07 59.2 m 3.8 m 29.5% 3.4 h 2.4 h INFO 15:37:58,561 TraversalEngine - chr5:140844850-140847441:1509 1.57e+07 59.7 m 3.8 m 29.8% 3.3 h 2.3 h INFO 15:38:28,594 TraversalEngine - chr5:148592910-148593131:179 1.58e+07 60.2 m 3.8 m 30.1% 3.3 h 2.3 h INFO 15:38:58,643 TraversalEngine - chr5:153810769-153811041:165 1.60e+07 60.7 m 3.8 m 30.3% 3.3 h 2.3 h INFO 15:39:28,802 TraversalEngine - chr5:168947924-168948232:156 1.61e+07 61.2 m 3.8 m 30.6% 3.3 h 2.3 h INFO 15:39:58,927 TraversalEngine - chr5:176452670-176453457:378 1.62e+07 61.7 m 3.8 m 30.8% 3.3 h 2.3 h INFO 15:40:28,963 TraversalEngine - chr5:179676295-179676739:163 1.64e+07 62.2 m 3.8 m 31.1% 3.3 h 2.3 h INFO 15:40:59,032 TraversalEngine - chr6:7844733-7844988:8 1.65e+07 62.7 m 3.8 m 31.4% 3.3 h 2.3 h INFO 15:41:29,065 TraversalEngine - chr6:24588013-24588241:131 1.66e+07 63.2 m 3.8 m 31.6% 3.3 h 2.3 h INFO 15:41:59,327 TraversalEngine - chr6:30020740-30021112:204 1.68e+07 63.8 m 3.8 m 31.9% 3.3 h 2.3 h INFO 15:42:29,524 TraversalEngine - chr6:31835106-31835343:16 1.70e+07 64.3 m 3.8 m 32.2% 3.3 h 2.3 h INFO 15:42:59,586 TraversalEngine - chr6:33344694-33345019:249 1.71e+07 64.8 m 3.8 m 32.5% 3.3 h 2.2 h INFO 15:43:29,595 TraversalEngine - chr6:36451551-36451865:38 1.73e+07 65.3 m 3.8 m 32.8% 3.3 h 2.2 h INFO 15:43:59,709 TraversalEngine - chr6:41820038-41820599:201 1.74e+07 65.8 m 3.8 m 33.0% 3.3 h 2.2 h INFO 15:44:29,950 TraversalEngine - chr6:43856372-43856644:62 1.75e+07 66.3 m 3.8 m 33.3% 3.3 h 2.2 h INFO 15:45:00,195 TraversalEngine - chr6:52237270-52237618:102 1.77e+07 66.8 m 3.8 m 33.6% 3.3 h 2.2 h INFO 15:45:30,470 TraversalEngine - chr6:71038414-71038587:67 1.78e+07 67.3 m 3.8 m 33.8% 3.3 h 2.2 h INFO 15:46:00,735 TraversalEngine - chr6:82971218-82971469:45 1.79e+07 67.8 m 3.8 m 34.1% 3.3 h 2.2 h INFO 15:46:30,841 TraversalEngine - chr6:91319823-91320101:254 1.81e+07 68.3 m 3.8 m 34.3% 3.3 h 2.2 h INFO 15:47:01,084 TraversalEngine - chr6:108608145-108608391:35 1.82e+07 68.8 m 3.8 m 34.6% 3.3 h 2.2 h INFO 15:47:31,113 TraversalEngine - chr6:117153532-117153807:77 1.83e+07 69.3 m 3.8 m 34.8% 3.3 h 2.2 h INFO 15:48:01,362 TraversalEngine - chr6:129827053-129827365:120 1.85e+07 69.8 m 3.8 m 35.1% 3.3 h 2.2 h INFO 15:48:31,510 TraversalEngine - chr6:137067866-137068039:76 1.86e+07 70.3 m 3.8 m 35.3% 3.3 h 2.1 h INFO 15:49:01,578 TraversalEngine - chr6:150039014-150039270:26 1.87e+07 70.8 m 3.8 m 35.6% 3.3 h 2.1 h INFO 15:49:31,587 TraversalEngine - chr6:155759587-155759863:58 1.89e+07 71.3 m 3.8 m 35.9% 3.3 h 2.1 h INFO 15:50:01,822 TraversalEngine - chr6:161456070-161456399:75 1.90e+07 71.8 m 3.8 m 36.1% 3.3 h 2.1 h INFO 15:50:31,987 TraversalEngine - chr7:1555941-1556182:93 1.91e+07 72.3 m 3.8 m 36.3% 3.3 h 2.1 h INFO 15:51:02,029 TraversalEngine - chr7:6785691-6785955:123 1.93e+07 72.8 m 3.8 m 36.6% 3.3 h 2.1 h INFO 15:51:32,212 TraversalEngine - chr7:26202471-26203237:192 1.94e+07 73.3 m 3.8 m 36.8% 3.3 h 2.1 h INFO 15:52:02,416 TraversalEngine - chr7:36303052-36303396:104 1.95e+07 73.8 m 3.8 m 37.1% 3.3 h 2.1 h INFO 15:52:32,567 TraversalEngine - chr7:44700473-44700775:144 1.96e+07 74.3 m 3.8 m 37.3% 3.3 h 2.1 h INFO 15:53:02,657 TraversalEngine - chr7:64079125-64079308:171 1.98e+07 74.8 m 3.8 m 37.5% 3.3 h 2.1 h INFO 15:53:32,720 TraversalEngine - chr7:73848862-73850615:1495 1.99e+07 75.3 m 3.8 m 37.8% 3.3 h 2.1 h INFO 15:54:02,820 TraversalEngine - chr7:86347648-86347857:112 2.00e+07 75.8 m 3.8 m 38.0% 3.3 h 2.1 h INFO 15:54:32,913 TraversalEngine - chr7:92905233-92905593:311 2.02e+07 76.3 m 3.8 m 38.3% 3.3 h 2.1 h INFO 15:55:02,977 TraversalEngine - chr7:98982170-98984041:106 2.03e+07 76.8 m 3.8 m 38.5% 3.3 h 2.0 h INFO 15:55:33,139 TraversalEngine - chr7:100481539-100482038:422 2.04e+07 77.3 m 3.8 m 38.8% 3.3 h 2.0 h INFO 15:56:03,170 TraversalEngine - chr7:106295168-106297312:936 2.06e+07 77.8 m 3.8 m 39.1% 3.3 h 2.0 h INFO 15:56:33,311 TraversalEngine - chr7:117162128-117162465:246 2.07e+07 78.3 m 3.8 m 39.3% 3.3 h 2.0 h INFO 15:57:03,450 TraversalEngine - chr7:128594401-128594712:236 2.08e+07 78.8 m 3.8 m 39.6% 3.3 h 2.0 h INFO 15:57:33,491 TraversalEngine - chr7:135026414-135026688:162 2.10e+07 79.3 m 3.8 m 39.8% 3.3 h 120.0 m INFO 15:58:03,628 TraversalEngine - chr7:142332671-142333033:138 2.11e+07 79.8 m 3.8 m 40.0% 3.3 h 119.6 m INFO 15:58:33,908 TraversalEngine - chr7:150445581-150445872:76 2.12e+07 80.3 m 3.8 m 40.3% 3.3 h 118.8 m INFO 15:59:03,977 TraversalEngine - chr8:1892247-1892911:26 2.14e+07 80.8 m 3.8 m 40.6% 3.3 h 118.3 m INFO 15:59:34,179 TraversalEngine - chr8:17961055-17961567:248 2.15e+07 81.3 m 3.8 m 40.9% 3.3 h 117.8 m INFO 16:00:04,246 TraversalEngine - chr8:24317386-24317621:234 2.16e+07 81.8 m 3.8 m 41.1% 3.3 h 117.3 m INFO 16:00:34,250 TraversalEngine - chr8:30818987-30826150:1665 2.18e+07 82.3 m 3.8 m 41.3% 3.3 h 116.9 m INFO 16:01:04,468 TraversalEngine - chr8:41702361-41702696:66 2.19e+07 82.8 m 3.8 m 41.6% 3.3 h 116.4 m INFO 16:01:34,545 TraversalEngine - chr8:59645925-59646153:15 2.20e+07 83.3 m 3.8 m 41.8% 3.3 h 115.8 m INFO 16:02:04,549 TraversalEngine - chr8:72374352-72374584:113 2.22e+07 83.8 m 3.8 m 42.1% 3.3 h 115.4 m INFO 16:02:34,594 TraversalEngine - chr8:91126178-91126474:138 2.23e+07 84.3 m 3.8 m 42.3% 3.3 h 115.0 m INFO 16:03:04,653 TraversalEngine - chr8:101259145-101259420:45 2.24e+07 84.8 m 3.8 m 42.6% 3.3 h 114.5 m INFO 16:03:34,728 TraversalEngine - chr8:116495352-116496563:932 2.25e+07 85.3 m 3.8 m 42.8% 3.3 h 114.0 m INFO 16:04:04,934 TraversalEngine - chr8:125575180-125575456:269 2.27e+07 85.8 m 3.8 m 43.1% 3.3 h 113.5 m INFO 16:04:35,145 TraversalEngine - chr8:141628320-141628654:26 2.28e+07 86.3 m 3.8 m 43.3% 3.3 h 113.1 m INFO 16:05:05,212 TraversalEngine - chr8:146046778-146047602:360 2.30e+07 86.8 m 3.8 m 43.7% 3.3 h 112.0 m INFO 16:05:35,276 TraversalEngine - chr9:8321507-8321811:208 2.31e+07 87.4 m 3.8 m 43.9% 3.3 h 111.5 m INFO 16:06:05,552 TraversalEngine - chr9:26974180-26974632:232 2.33e+07 87.9 m 3.8 m 44.2% 3.3 h 111.0 m INFO 16:06:35,657 TraversalEngine - chr9:35090854-35092266:595 2.34e+07 88.4 m 3.8 m 44.4% 3.3 h 110.6 m INFO 16:07:05,978 TraversalEngine - chr9:42366182-42366438:132 2.35e+07 88.9 m 3.8 m 44.7% 3.3 h 109.9 m INFO 16:07:35,992 TraversalEngine - chr9:76587340-76587664:72 2.37e+07 89.4 m 3.8 m 44.9% 3.3 h 109.5 m INFO 16:08:06,109 TraversalEngine - chr9:88109516-88109757:119 2.38e+07 89.9 m 3.8 m 45.2% 3.3 h 109.1 m INFO 16:08:36,168 TraversalEngine - chr9:96913491-96913815:308 2.39e+07 90.4 m 3.8 m 45.4% 3.3 h 108.6 m INFO 16:09:06,239 TraversalEngine - chr9:102102596-102102852:2 2.41e+07 90.9 m 3.8 m 45.7% 3.3 h 108.1 m INFO 16:09:36,302 TraversalEngine - chr9:112743447-112744344:36 2.42e+07 91.4 m 3.8 m 45.9% 3.3 h 107.6 m INFO 16:10:06,407 TraversalEngine - chr9:118169670-118169929:42 2.43e+07 91.9 m 3.8 m 46.2% 3.3 h 107.1 m INFO 16:10:36,677 TraversalEngine - chr9:125814374-125814643:14 2.45e+07 92.4 m 3.8 m 46.4% 3.3 h 106.5 m INFO 16:11:06,717 TraversalEngine - chr9:129868616-129869276:532 2.46e+07 92.9 m 3.8 m 46.7% 3.3 h 106.1 m INFO 16:11:36,939 TraversalEngine - chr9:131541636-131542035:380 2.47e+07 93.4 m 3.8 m 46.9% 3.3 h 105.6 m INFO 16:12:07,017 TraversalEngine - chr9:135198101-135198440:171 2.49e+07 93.9 m 3.8 m 47.2% 3.3 h 105.1 m INFO 16:12:37,042 TraversalEngine - chr9:138351644-138351917:16 2.50e+07 94.4 m 3.8 m 47.4% 3.3 h 104.7 m INFO 16:13:07,108 TraversalEngine - chr9:139591668-139591951:228 2.51e+07 94.9 m 3.8 m 47.7% 3.3 h 104.0 m INFO 16:13:37,398 TraversalEngine - chr10:7809597-7809872:50 2.53e+07 95.4 m 3.8 m 48.0% 3.3 h 103.5 m INFO 16:14:07,536 TraversalEngine - chr10:17019522-17019864:64 2.54e+07 95.9 m 3.8 m 48.2% 3.3 h 103.1 m INFO 16:14:37,676 TraversalEngine - chr10:25901509-25901897:14 2.55e+07 96.4 m 3.8 m 48.4% 3.3 h 102.7 m INFO 16:15:07,907 TraversalEngine - chr10:33254730-33255118:181 2.56e+07 96.9 m 3.8 m 48.7% 3.3 h 102.2 m INFO 16:15:37,913 TraversalEngine - chr10:49110089-49110413:50 2.58e+07 97.4 m 3.8 m 48.9% 3.3 h 101.7 m INFO 16:16:08,058 TraversalEngine - chr10:61691548-61691796:73 2.59e+07 97.9 m 3.8 m 49.2% 3.3 h 101.2 m INFO 16:16:38,339 TraversalEngine - chr10:71635951-71636170:143 2.60e+07 98.4 m 3.8 m 49.4% 3.3 h 100.6 m INFO 16:17:08,417 TraversalEngine - chr10:76272547-76273317:223 2.62e+07 98.9 m 3.8 m 49.7% 3.3 h 100.1 m INFO 16:17:38,511 TraversalEngine - chr10:88843987-88844581:389 2.63e+07 99.4 m 3.8 m 49.9% 3.3 h 99.7 m INFO 16:18:08,539 TraversalEngine - chr10:95062692-95063032:80 2.64e+07 99.9 m 3.8 m 50.2% 3.3 h 99.2 m INFO 16:18:38,754 TraversalEngine - chr10:98754365-98754645:40 2.66e+07 100.4 m 3.8 m 50.4% 3.3 h 98.7 m INFO 16:19:08,754 TraversalEngine - chr10:102251926-102252306:40 2.67e+07 100.9 m 3.8 m 50.7% 3.3 h 98.3 m INFO 16:19:38,847 TraversalEngine - chr10:105134998-105135312:239 2.68e+07 101.4 m 3.8 m 50.9% 3.3 h 97.7 m INFO 16:20:09,005 TraversalEngine - chr10:114171620-114171858:155 2.69e+07 101.9 m 3.8 m 51.2% 3.3 h 97.3 m INFO 16:20:39,096 TraversalEngine - chr10:120479711-120479987:126 2.71e+07 102.4 m 3.8 m 51.4% 3.3 h 96.8 m INFO 16:21:09,248 TraversalEngine - chr10:126663258-126663626:293 2.72e+07 102.9 m 3.8 m 51.6% 3.3 h 96.4 m INFO 16:21:39,312 TraversalEngine - chr10:135223510-135223687:147 2.73e+07 103.4 m 3.8 m 51.9% 3.3 h 95.9 m INFO 16:22:09,383 TraversalEngine - chr11:2861735-2862015:25 2.75e+07 103.9 m 3.8 m 52.2% 3.3 h 95.3 m INFO 16:22:39,413 TraversalEngine - chr11:6608785-6609289:145 2.76e+07 104.4 m 3.8 m 52.5% 3.3 h 94.5 m INFO 16:23:09,563 TraversalEngine - chr11:11599407-11599791:80 2.78e+07 104.9 m 3.8 m 52.8% 3.3 h 93.9 m INFO 16:23:39,598 TraversalEngine - chr11:18289962-18290222:16 2.79e+07 105.4 m 3.8 m 53.0% 3.3 h 93.5 m INFO 16:24:09,759 TraversalEngine - chr11:31768759-31769059:229 2.80e+07 105.9 m 3.8 m 53.3% 3.3 h 93.0 m INFO 16:24:39,778 TraversalEngine - chr11:44242905-44243384:68 2.82e+07 106.4 m 3.8 m 53.5% 3.3 h 92.5 m INFO 16:25:09,835 TraversalEngine - chr11:47670156-47670459:27 2.83e+07 106.9 m 3.8 m 53.8% 3.3 h 92.0 m INFO 16:25:39,992 TraversalEngine - chr11:59321257-59321490:38 2.85e+07 107.4 m 3.8 m 54.1% 3.3 h 91.1 m INFO 16:26:10,046 TraversalEngine - chr11:61716029-61716366:97 2.86e+07 107.9 m 3.8 m 54.3% 3.3 h 90.7 m INFO 16:26:40,078 TraversalEngine - chr11:63813116-63813488:15 2.88e+07 108.4 m 3.8 m 54.7% 3.3 h 90.0 m INFO 16:27:10,254 TraversalEngine - chr11:65387382-65388023:202 2.90e+07 108.9 m 3.8 m 55.0% 3.3 h 89.2 m INFO 16:27:40,281 TraversalEngine - chr11:67155577-67156016:382 2.91e+07 109.4 m 3.8 m 55.3% 3.3 h 88.5 m INFO 16:28:10,621 TraversalEngine - chr11:72076306-72076506:49 2.93e+07 109.9 m 3.8 m 55.5% 3.3 h 88.0 m INFO 16:28:40,822 TraversalEngine - chr11:76737857-76738055:28 2.94e+07 110.4 m 3.8 m 55.8% 3.3 h 87.5 m INFO 16:29:10,858 TraversalEngine - chr11:92526847-92527166:301 2.95e+07 110.9 m 3.8 m 56.0% 3.3 h 87.1 m INFO 16:29:41,056 TraversalEngine - chr11:107304430-107304806:246 2.96e+07 111.4 m 3.8 m 56.3% 3.3 h 86.6 m INFO 16:30:11,233 TraversalEngine - chr11:113778685-113778922:168 2.98e+07 111.9 m 3.8 m 56.5% 3.3 h 86.1 m INFO 16:30:41,279 TraversalEngine - chr11:118007765-118008298:479 2.99e+07 112.5 m 3.8 m 56.8% 3.3 h 85.6 m INFO 16:31:11,501 TraversalEngine - chr11:123018289-123018664:16 3.00e+07 113.0 m 3.8 m 57.1% 3.3 h 85.0 m INFO 16:31:41,602 TraversalEngine - chr11:129848077-129849001:279 3.02e+07 113.5 m 3.8 m 57.3% 3.3 h 84.4 m INFO 16:32:11,832 TraversalEngine - chr12:4496413-4496691:125 3.03e+07 114.0 m 3.8 m 57.6% 3.3 h 84.0 m INFO 16:32:42,051 TraversalEngine - chr12:7174437-7174650:12 3.05e+07 114.5 m 3.8 m 57.9% 3.3 h 83.4 m INFO 16:33:12,208 TraversalEngine - chr12:10671432-10671665:135 3.06e+07 115.0 m 3.8 m 58.1% 3.3 h 83.0 m INFO 16:33:42,240 TraversalEngine - chr12:20781233-20781548:272 3.07e+07 115.5 m 3.8 m 58.3% 3.3 h 82.5 m INFO 16:34:12,242 TraversalEngine - chr12:27736716-27737157:366 3.08e+07 116.0 m 3.8 m 58.6% 3.3 h 82.1 m INFO 16:34:42,332 TraversalEngine - chr12:40798994-40799315:89 3.10e+07 116.5 m 3.8 m 58.8% 3.3 h 81.6 m INFO 16:35:12,499 TraversalEngine - chr12:47519819-47520231:63 3.11e+07 117.0 m 3.8 m 59.1% 3.3 h 81.1 m INFO 16:35:42,899 TraversalEngine - chr12:49787211-49787471:27 3.12e+07 117.5 m 3.8 m 59.3% 3.3 h 80.6 m INFO 16:36:12,945 TraversalEngine - chr12:51839863-51840064:51 3.14e+07 118.0 m 3.8 m 59.6% 3.3 h 80.1 m INFO 16:36:42,949 TraversalEngine - chr12:54670658-54670930:92 3.15e+07 118.5 m 3.8 m 59.8% 3.3 h 79.5 m INFO 16:37:13,005 TraversalEngine - chr12:55924891-55925090:189 3.17e+07 119.0 m 3.8 m 60.1% 3.3 h 79.0 m INFO 16:37:43,027 TraversalEngine - chr12:63396713-63396941:95 3.18e+07 119.5 m 3.8 m 60.4% 3.3 h 78.4 m INFO 16:38:13,354 TraversalEngine - chr12:73969593-73969897:154 3.19e+07 120.0 m 3.8 m 60.6% 3.3 h 77.9 m INFO 16:38:43,504 TraversalEngine - chr12:92596607-92597054:166 3.21e+07 2.0 h 3.8 m 60.9% 3.3 h 77.5 m INFO 16:39:13,539 TraversalEngine - chr12:100204155-100204493:240 3.22e+07 2.0 h 3.8 m 61.1% 3.3 h 77.0 m INFO 16:39:43,598 TraversalEngine - chr12:105232191-105232476:103 3.23e+07 2.0 h 3.8 m 61.3% 3.3 h 76.6 m INFO 16:40:13,704 TraversalEngine - chr12:109249666-109250280:454 3.24e+07 2.0 h 3.8 m 61.6% 3.3 h 76.1 m INFO 16:40:43,885 TraversalEngine - chr12:112385303-112385820:182 3.26e+07 2.0 h 3.8 m 61.8% 3.3 h 75.7 m INFO 16:41:14,033 TraversalEngine - chr12:119915631-119915967:273 3.27e+07 2.0 h 3.8 m 62.1% 3.3 h 75.2 m INFO 16:41:44,274 TraversalEngine - chr12:122710220-122710810:525 3.28e+07 2.1 h 3.8 m 62.3% 3.3 h 74.7 m INFO 16:42:14,406 TraversalEngine - chr12:131722476-131722758:192 3.30e+07 2.1 h 3.8 m 62.6% 3.3 h 74.2 m INFO 16:42:44,582 TraversalEngine - chr13:24315807-24316184:299 3.31e+07 2.1 h 3.8 m 62.8% 3.3 h 73.6 m INFO 16:43:14,678 TraversalEngine - chr13:31721588-31721899:253 3.32e+07 2.1 h 3.8 m 63.1% 3.3 h 73.1 m INFO 16:43:44,766 TraversalEngine - chr13:41163381-41163656:2 3.34e+07 2.1 h 3.8 m 63.4% 3.3 h 72.6 m INFO 16:44:14,995 TraversalEngine - chr13:49013738-49014039:51 3.35e+07 2.1 h 3.8 m 63.6% 3.3 h 72.1 m INFO 16:44:45,100 TraversalEngine - chr13:76472519-76473180:410 3.36e+07 2.1 h 3.8 m 63.9% 3.3 h 71.6 m INFO 16:45:15,169 TraversalEngine - chr13:98156314-98156583:253 3.38e+07 2.1 h 3.8 m 64.1% 3.3 h 71.1 m INFO 16:45:45,239 TraversalEngine - chr13:110683478-110683716:174 3.39e+07 2.1 h 3.8 m 64.4% 3.3 h 70.6 m INFO 16:46:15,307 TraversalEngine - chr14:19994592-19995582:65 3.40e+07 2.1 h 3.8 m 64.6% 3.3 h 70.1 m INFO 16:46:45,414 TraversalEngine - chr14:23529156-23529483:227 3.42e+07 2.1 h 3.8 m 64.9% 3.3 h 69.5 m INFO 16:47:15,504 TraversalEngine - chr14:32360284-32363805:520 3.43e+07 2.2 h 3.8 m 65.2% 3.3 h 68.9 m INFO 16:47:45,759 TraversalEngine - chr14:49190383-49190757:63 3.45e+07 2.2 h 3.8 m 65.5% 3.3 h 68.3 m INFO 16:48:15,821 TraversalEngine - chr14:54599014-54599871:131 3.46e+07 2.2 h 3.8 m 65.7% 3.3 h 67.9 m INFO 16:48:45,896 TraversalEngine - chr14:63610364-63610682:264 3.47e+07 2.2 h 3.8 m 66.0% 3.3 h 67.3 m INFO 16:49:16,191 TraversalEngine - chr14:68875922-68876164:123 3.49e+07 2.2 h 3.8 m 66.2% 3.3 h 66.9 m INFO 16:49:46,330 TraversalEngine - chr14:74046472-74046744:127 3.50e+07 2.2 h 3.8 m 66.5% 3.3 h 66.3 m INFO 16:50:16,353 TraversalEngine - chr14:80644634-80644853:160 3.51e+07 2.2 h 3.8 m 66.7% 3.3 h 65.9 m INFO 16:50:46,528 TraversalEngine - chr14:92467273-92467875:15 3.53e+07 2.2 h 3.8 m 67.0% 3.3 h 65.4 m INFO 16:51:16,660 TraversalEngine - chr14:99401529-99401811:2 3.54e+07 2.2 h 3.8 m 67.2% 3.3 h 64.9 m INFO 16:51:46,780 TraversalEngine - chr14:104308052-104308304:146 3.55e+07 2.2 h 3.8 m 67.5% 3.3 h 64.3 m INFO 16:52:16,869 TraversalEngine - chr15:27799779-27800279:179 3.57e+07 2.2 h 3.8 m 67.7% 3.3 h 63.8 m INFO 16:52:46,970 TraversalEngine - chr15:38377980-38378532:324 3.58e+07 2.2 h 3.8 m 68.0% 3.3 h 63.3 m INFO 16:53:16,973 TraversalEngine - chr15:40340373-40340567:152 3.60e+07 2.3 h 3.8 m 68.3% 3.3 h 62.8 m INFO 16:53:47,028 TraversalEngine - chr15:41894360-41894639:211 3.61e+07 2.3 h 3.8 m 68.5% 3.3 h 62.2 m INFO 16:54:17,084 TraversalEngine - chr15:47095974-47096579:147 3.62e+07 2.3 h 3.8 m 68.8% 3.3 h 61.8 m INFO 16:54:47,311 TraversalEngine - chr15:51693080-51693321:117 3.63e+07 2.3 h 3.8 m 69.0% 3.3 h 61.3 m INFO 16:55:17,565 TraversalEngine - chr15:60052041-60052330:61 3.65e+07 2.3 h 3.8 m 69.3% 3.3 h 60.8 m INFO 16:55:47,597 TraversalEngine - chr15:64411192-64411487:76 3.66e+07 2.3 h 3.8 m 69.5% 3.3 h 60.3 m INFO 16:56:17,774 TraversalEngine - chr15:70810624-70811195:327 3.67e+07 2.3 h 3.8 m 69.7% 3.3 h 59.9 m INFO 16:56:47,952 TraversalEngine - chr15:74365692-74365952:209 3.69e+07 2.3 h 3.8 m 70.0% 3.3 h 59.3 m INFO 16:57:17,983 TraversalEngine - chr15:81722632-81724646:547 3.70e+07 2.3 h 3.8 m 70.3% 3.3 h 58.8 m INFO 16:57:48,087 TraversalEngine - chr15:88792734-88793047:33 3.72e+07 2.3 h 3.8 m 70.6% 3.3 h 58.3 m INFO 16:58:18,195 TraversalEngine - chr15:100004376-100004700:84 3.73e+07 2.3 h 3.8 m 70.8% 3.3 h 57.8 m INFO 16:58:48,223 TraversalEngine - chr16:1754042-1754536:118 3.75e+07 2.3 h 3.8 m 71.1% 3.3 h 57.1 m INFO 16:59:18,224 TraversalEngine - chr16:3194173-3195261:174 3.76e+07 2.4 h 3.7 m 71.4% 3.3 h 56.4 m INFO 16:59:48,296 TraversalEngine - chr16:8903664-8903915:212 3.78e+07 2.4 h 3.7 m 71.7% 3.3 h 55.8 m INFO 17:00:18,383 TraversalEngine - chr16:16174567-16174837:151 3.79e+07 2.4 h 3.7 m 72.0% 3.3 h 55.4 m INFO 17:00:48,392 TraversalEngine - chr16:21053006-21053351:49 3.80e+07 2.4 h 3.7 m 72.2% 3.3 h 54.9 m INFO 17:01:18,613 TraversalEngine - chr16:27363924-27364173:219 3.82e+07 2.4 h 3.7 m 72.5% 3.3 h 54.4 m INFO 17:01:48,642 TraversalEngine - chr16:30297181-30297597:198 3.83e+07 2.4 h 3.7 m 72.8% 3.3 h 53.8 m INFO 17:02:18,866 TraversalEngine - chr16:46242168-46242408:164 3.85e+07 2.4 h 3.7 m 73.1% 3.3 h 53.1 m INFO 17:02:48,931 TraversalEngine - chr16:55224070-55224247:49 3.86e+07 2.4 h 3.7 m 73.3% 3.3 h 52.6 m INFO 17:03:18,961 TraversalEngine - chr16:57129221-57129746:181 3.87e+07 2.4 h 3.7 m 73.6% 3.3 h 52.1 m INFO 17:03:49,054 TraversalEngine - chr16:66433884-66434978:293 3.89e+07 2.4 h 3.7 m 73.9% 3.3 h 51.5 m INFO 17:04:19,221 TraversalEngine - chr16:69145775-69146076:275 3.90e+07 2.4 h 3.7 m 74.1% 3.3 h 51.0 m INFO 17:04:49,373 TraversalEngine - chr16:73590996-73591569:526 3.92e+07 2.4 h 3.7 m 74.4% 3.3 h 50.5 m INFO 17:05:19,653 TraversalEngine - chr16:83679308-83679507:54 3.93e+07 2.5 h 3.7 m 74.6% 3.3 h 50.0 m INFO 17:05:49,805 TraversalEngine - chr16:88494469-88494778:203 3.95e+07 2.5 h 3.7 m 74.9% 3.3 h 49.4 m INFO 17:06:19,982 TraversalEngine - chr17:3498815-3499049:156 3.96e+07 2.5 h 3.7 m 75.2% 3.3 h 48.9 m INFO 17:06:50,256 TraversalEngine - chr17:5012711-5013149:19 3.97e+07 2.5 h 3.7 m 75.5% 3.3 h 48.3 m INFO 17:07:20,367 TraversalEngine - chr17:7431393-7431668:256 3.99e+07 2.5 h 3.7 m 75.8% 3.3 h 47.7 m INFO 17:07:50,572 TraversalEngine - chr17:9479372-9479673:218 4.01e+07 2.5 h 3.7 m 76.1% 3.3 h 47.1 m INFO 17:08:20,619 TraversalEngine - chr17:16015767-16016109:153 4.02e+07 2.5 h 3.7 m 76.3% 3.3 h 46.6 m INFO 17:08:50,844 TraversalEngine - chr17:19421157-19421533:51 4.03e+07 2.5 h 3.7 m 76.6% 3.3 h 46.0 m INFO 17:09:21,011 TraversalEngine - chr17:24601251-24601519:25 4.05e+07 2.5 h 3.7 m 76.9% 3.3 h 45.5 m INFO 17:09:51,123 TraversalEngine - chr17:28118692-28118958:61 4.06e+07 2.5 h 3.7 m 77.1% 3.3 h 45.0 m INFO 17:10:21,182 TraversalEngine - chr17:32675542-32675838:44 4.07e+07 2.5 h 3.7 m 77.4% 3.3 h 44.5 m INFO 17:10:51,400 TraversalEngine - chr17:35598911-35599228:269 4.09e+07 2.5 h 3.7 m 77.6% 3.3 h 44.0 m INFO 17:11:21,483 TraversalEngine - chr17:37525499-37525989:126 4.10e+07 2.6 h 3.7 m 77.9% 3.3 h 43.5 m INFO 17:11:51,633 TraversalEngine - chr17:39441267-39441570:51 4.12e+07 2.6 h 3.7 m 78.2% 3.3 h 42.9 m INFO 17:12:22,041 TraversalEngine - chr17:42574519-42574876:107 4.13e+07 2.6 h 3.7 m 78.4% 3.3 h 42.4 m INFO 17:12:52,164 TraversalEngine - chr17:45787139-45787491:201 4.14e+07 2.6 h 3.7 m 78.7% 3.3 h 41.9 m INFO 17:13:22,321 TraversalEngine - chr17:53699634-53700021:31 4.16e+07 2.6 h 3.7 m 78.9% 3.3 h 41.4 m INFO 17:13:52,507 TraversalEngine - chr17:57216338-57216642:112 4.17e+07 2.6 h 3.7 m 79.2% 3.3 h 40.9 m INFO 17:14:22,515 TraversalEngine - chr17:62215344-62215634:91 4.18e+07 2.6 h 3.7 m 79.4% 3.3 h 40.4 m INFO 17:14:52,536 TraversalEngine - chr17:68713813-68714071:118 4.20e+07 2.6 h 3.7 m 79.7% 3.3 h 39.9 m INFO 17:15:22,716 TraversalEngine - chr17:71486135-71486444:279 4.21e+07 2.6 h 3.7 m 80.0% 3.3 h 39.4 m INFO 17:15:52,993 TraversalEngine - chr17:75725705-75725970:124 4.23e+07 2.6 h 3.7 m 80.2% 3.3 h 38.8 m INFO 17:16:23,175 TraversalEngine - chr17:77803524-77803844:212 4.24e+07 2.6 h 3.7 m 80.5% 3.3 h 38.3 m INFO 17:16:53,385 TraversalEngine - chr18:8626176-8626430:68 4.25e+07 2.6 h 3.7 m 80.8% 3.3 h 37.8 m INFO 17:17:23,636 TraversalEngine - chr18:19363522-19363749:86 4.27e+07 2.7 h 3.7 m 81.0% 3.3 h 37.3 m INFO 17:17:53,814 TraversalEngine - chr18:28575814-28576085:5 4.28e+07 2.7 h 3.7 m 81.3% 3.3 h 36.8 m INFO 17:18:23,997 TraversalEngine - chr18:43625957-43626244:3 4.29e+07 2.7 h 3.7 m 81.5% 3.3 h 36.3 m INFO 17:18:54,210 TraversalEngine - chr18:55156694-55157240:44 4.31e+07 2.7 h 3.7 m 81.8% 3.3 h 35.8 m INFO 17:19:24,356 TraversalEngine - chr18:75236307-75236489:82 4.32e+07 2.7 h 3.7 m 82.0% 3.3 h 35.3 m INFO 17:19:54,385 TraversalEngine - chr19:1458922-1459183:89 4.34e+07 2.7 h 3.7 m 82.3% 3.3 h 34.7 m INFO 17:20:24,417 TraversalEngine - chr19:3998675-3999317:410 4.35e+07 2.7 h 3.7 m 82.6% 3.3 h 34.2 m INFO 17:20:54,531 TraversalEngine - chr19:6415638-6415869:218 4.36e+07 2.7 h 3.7 m 82.9% 3.3 h 33.6 m INFO 17:21:24,713 TraversalEngine - chr19:8374222-8374517:266 4.38e+07 2.7 h 3.7 m 83.2% 3.3 h 33.0 m INFO 17:21:54,773 TraversalEngine - chr19:10880704-10880958:133 4.40e+07 2.7 h 3.7 m 83.5% 3.3 h 32.4 m INFO 17:22:24,789 TraversalEngine - chr19:12919916-12920702:540 4.41e+07 2.7 h 3.7 m 83.7% 3.3 h 31.9 m INFO 17:22:54,833 TraversalEngine - chr19:15851339-15851782:181 4.43e+07 2.7 h 3.7 m 84.0% 3.3 h 31.3 m INFO 17:23:24,973 TraversalEngine - chr19:18137895-18138187:248 4.44e+07 2.8 h 3.7 m 84.3% 3.3 h 30.7 m INFO 17:23:54,995 TraversalEngine - chr19:20995372-20995524:86 4.46e+07 2.8 h 3.7 m 84.6% 3.3 h 30.2 m INFO 17:24:25,301 TraversalEngine - chr19:40302046-40302235:82 4.47e+07 2.8 h 3.7 m 84.9% 3.3 h 29.7 m INFO 17:24:55,408 TraversalEngine - chr19:42747265-42749108:740 4.48e+07 2.8 h 3.7 m 85.2% 3.3 h 29.1 m INFO 17:25:25,528 TraversalEngine - chr19:44647203-44647604:50 4.50e+07 2.8 h 3.7 m 85.4% 3.3 h 28.5 m INFO 17:25:55,757 TraversalEngine - chr19:47033774-47034250:143 4.51e+07 2.8 h 3.7 m 85.7% 3.3 h 27.9 m INFO 17:26:25,772 TraversalEngine - chr19:49975927-49976223:170 4.53e+07 2.8 h 3.7 m 86.0% 3.3 h 27.3 m INFO 17:26:56,069 TraversalEngine - chr19:52453581-52453835:14 4.55e+07 2.8 h 3.7 m 86.3% 3.3 h 26.7 m INFO 17:27:26,117 TraversalEngine - chr19:54281409-54281705:217 4.56e+07 2.8 h 3.7 m 86.6% 3.3 h 26.2 m INFO 17:27:56,186 TraversalEngine - chr19:55993089-55993592:480 4.58e+07 2.8 h 3.7 m 86.9% 3.3 h 25.6 m INFO 17:28:26,306 TraversalEngine - chr19:59318865-59319184:105 4.59e+07 2.8 h 3.7 m 87.2% 3.3 h 25.1 m INFO 17:28:56,438 TraversalEngine - chr19:60604541-60605017:256 4.60e+07 2.8 h 3.7 m 87.4% 3.3 h 24.6 m INFO 17:29:26,437 TraversalEngine - chr19:63714372-63715209:737 4.62e+07 2.9 h 3.7 m 87.8% 3.3 h 23.9 m INFO 17:29:56,602 TraversalEngine - chr20:3608064-3608293:21 4.64e+07 2.9 h 3.7 m 88.0% 3.3 h 23.3 m INFO 17:30:26,708 TraversalEngine - chr20:13645940-13646236:79 4.65e+07 2.9 h 3.7 m 88.3% 3.3 h 22.8 m INFO 17:30:56,785 TraversalEngine - chr20:25144237-25144422:26 4.66e+07 2.9 h 3.7 m 88.5% 3.3 h 22.4 m INFO 17:31:26,845 TraversalEngine - chr20:31723790-31723964:111 4.68e+07 2.9 h 3.7 m 88.8% 3.3 h 21.9 m INFO 17:31:57,142 TraversalEngine - chr20:34718102-34718424:21 4.69e+07 2.9 h 3.7 m 89.1% 3.3 h 21.4 m INFO 17:32:27,264 TraversalEngine - chr20:41665739-41666018:61 4.70e+07 2.9 h 3.7 m 89.3% 3.3 h 20.8 m INFO 17:32:57,295 TraversalEngine - chr20:44654375-44654650:163 4.72e+07 2.9 h 3.7 m 89.6% 3.3 h 20.3 m INFO 17:33:27,386 TraversalEngine - chr20:52016777-52017094:77 4.73e+07 2.9 h 3.7 m 89.9% 3.2 h 19.8 m INFO 17:33:57,637 TraversalEngine - chr20:60399347-60399979:205 4.75e+07 2.9 h 3.7 m 90.1% 3.2 h 19.2 m INFO 17:34:27,785 TraversalEngine - chr21:14669769-14670086:126 4.76e+07 2.9 h 3.7 m 90.4% 3.2 h 18.7 m INFO 17:34:57,924 TraversalEngine - chr21:32960049-32960391:115 4.78e+07 2.9 h 3.7 m 90.7% 3.2 h 18.2 m INFO 17:35:28,137 TraversalEngine - chr21:39469311-39469535:61 4.79e+07 3.0 h 3.7 m 90.9% 3.2 h 17.7 m INFO 17:35:58,256 TraversalEngine - chr21:43900821-43901121:29 4.80e+07 3.0 h 3.7 m 91.2% 3.2 h 17.2 m INFO 17:36:28,451 TraversalEngine - chr21:46382775-46383063:179 4.81e+07 3.0 h 3.7 m 91.4% 3.3 h 16.8 m INFO 17:36:58,507 TraversalEngine - chr22:18480011-18480832:271 4.83e+07 3.0 h 3.7 m 91.7% 3.3 h 16.3 m INFO 17:37:28,541 TraversalEngine - chr22:22903397-22903860:419 4.84e+07 3.0 h 3.7 m 91.9% 3.2 h 15.7 m INFO 17:37:58,699 TraversalEngine - chr22:28743841-28744136:276 4.85e+07 3.0 h 3.7 m 92.2% 3.2 h 15.3 m INFO 17:38:28,802 TraversalEngine - chr22:32107830-32108105:45 4.87e+07 3.0 h 3.7 m 92.4% 3.3 h 14.8 m INFO 17:38:58,849 TraversalEngine - chr22:36709235-36709812:179 4.88e+07 3.0 h 3.7 m 92.7% 3.2 h 14.2 m INFO 17:39:29,087 TraversalEngine - chr22:40069290-40069601:87 4.89e+07 3.0 h 3.7 m 92.9% 3.3 h 13.8 m INFO 17:39:59,222 TraversalEngine - chr22:43946070-43946303:96 4.91e+07 3.0 h 3.7 m 93.2% 3.3 h 13.3 m INFO 17:40:29,304 TraversalEngine - chr22:49233453-49234020:561 4.92e+07 3.0 h 3.7 m 93.5% 3.3 h 12.8 m INFO 17:40:59,337 TraversalEngine - chrX:11048873-11049109:104 4.94e+07 3.0 h 3.7 m 93.7% 3.2 h 12.2 m INFO 17:41:29,573 TraversalEngine - chrX:18677756-18678066:185 4.95e+07 3.1 h 3.7 m 94.0% 3.3 h 11.8 m INFO 17:41:59,644 TraversalEngine - chrX:29210901-29211330:146 4.96e+07 3.1 h 3.7 m 94.2% 3.3 h 11.3 m INFO 17:42:29,890 TraversalEngine - chrX:43427630-43427874:213 4.98e+07 3.1 h 3.7 m 94.5% 3.3 h 10.8 m INFO 17:43:00,035 TraversalEngine - chrX:48777849-48778074:113 4.99e+07 3.1 h 3.7 m 94.7% 3.3 h 10.3 m INFO 17:43:30,140 TraversalEngine - chrX:53671011-53671266:236 5.00e+07 3.1 h 3.7 m 95.0% 3.2 h 9.7 m INFO 17:44:00,286 TraversalEngine - chrX:69335771-69336031:13 5.02e+07 3.1 h 3.7 m 95.3% 3.2 h 9.2 m INFO 17:44:30,312 TraversalEngine - chrX:73657475-73657769:258 5.03e+07 3.1 h 3.7 m 95.5% 3.2 h 8.7 m INFO 17:45:00,557 TraversalEngine - chrX:99822805-99823063:46 5.05e+07 3.1 h 3.7 m 95.8% 3.2 h 8.2 m INFO 17:45:30,671 TraversalEngine - chrX:107206859-107207342:340 5.06e+07 3.1 h 3.7 m 96.1% 3.2 h 7.7 m INFO 17:46:00,813 TraversalEngine - chrX:118008386-118008626:178 5.07e+07 3.1 h 3.7 m 96.3% 3.3 h 7.2 m INFO 17:46:30,919 TraversalEngine - chrX:128873348-128873653:283 5.08e+07 3.1 h 3.7 m 96.5% 3.3 h 6.7 m INFO 17:47:00,943 TraversalEngine - chrX:135641852-135642072:136 5.10e+07 3.1 h 3.7 m 96.8% 3.3 h 6.3 m INFO 17:47:31,006 TraversalEngine - chrX:152590454-152590924:468 5.11e+07 3.2 h 3.7 m 97.1% 3.2 h 5.7 m INFO 17:48:01,082 TraversalEngine - chrX:154181217-154181727:32 5.13e+07 3.2 h 3.7 m 97.4% 3.2 h 5.1 m INFO 17:48:32,053 TraversalEngine - AluSg:49 5.20e+07 3.2 h 3.7 m 97.7% 3.2 h 4.5 m INFO 17:49:02,303 TraversalEngine - L1_L1_Homo_sapiens:1402 5.26e+07 3.2 h 3.6 m 98.5% 3.2 h 2.9 m INFO 17:49:32,310 TraversalEngine - LTR16A2_ERV3_Homo_sapiens:85 5.29e+07 3.2 h 3.6 m 99.0% 3.2 h 117.7 s INFO 17:50:02,377 TraversalEngine - MER6_Mariner_Tc1_Eutheria:124 5.34e+07 3.2 h 3.6 m 99.7% 3.2 h 40.2 s INFO 17:50:22,607 TraversalEngine - Total runtime 11528.36 secs, 192.14 min, 3.20 hours INFO 17:50:22,613 TraversalEngine - 2417941 reads were filtered out during traversal out of 37119559 total (6.51%) INFO 17:50:22,614 TraversalEngine - -> 2417941 reads (6.51% of total) failing MappingQualityZeroFilter INFO 17:50:26,841 GATKRunReport - Uploaded run statistics report to AWS S3 Script done on Thu 27 Sep 2012 05:50:33 PM EDT