INFO 06:54:14,926 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:54:14,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 INFO 06:54:14,933 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 06:54:14,933 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 06:54:14,938 HelpFormatter - Program Args: -T HaplotypeCaller -R /proj/b2013060/ReferenceTools/homo_sapiens_catHg19_bwa0.7.4.fa -I /proj/b2014226/nobackup/Lina_Results/150113_D00118_0176_BC5MHDANXX/FinalBAM/SS-pool-12-tag16.final.bam --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 --dontUseSoftClippedBases -o /proj/b2014226/nobackup/Lina_Results/haplotypeCaller/SS-pool-12-tag16.final.bam.g.vcf -rf BadCigar INFO 06:54:14,954 HelpFormatter - Executing as linah@m168.uppmax.uu.se on Linux 2.6.32-573.7.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_85-mockbuild_2015_07_22_14_52-b00. INFO 06:54:14,955 HelpFormatter - Date/Time: 2015/10/22 06:54:14 INFO 06:54:14,955 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:54:14,955 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:54:15,224 GenomeAnalysisEngine - Strictness is SILENT INFO 06:54:15,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 06:54:15,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:54:15,532 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13 INFO 06:54:15,556 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 06:54:15,762 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 06:54:15,790 GenomeAnalysisEngine - Done preparing for traversal INFO 06:54:15,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 06:54:15,791 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 06:54:15,792 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 06:54:15,792 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output INFO 06:54:15,793 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output INFO 06:54:16,081 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 06:54:22,333 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file INFO 06:54:22,348 VectorLoglessPairHMM - Using vectorized implementation of PairHMM INFO 06:54:45,809 ProgressMeter - chr6_cox_hap2:1413714 251858.0 30.0 s 119.0 s 0.1% 15.5 h 15.5 h INFO 06:55:45,810 ProgressMeter - chr6_cox_hap2:4033109 251858.0 90.0 s 6.0 m 0.1% 18.1 h 18.1 h INFO 06:56:45,812 ProgressMeter - chr1:7586011 5047229.0 2.5 m 29.0 s 0.4% 10.2 h 10.2 h INFO 06:57:15,813 ProgressMeter - chr1:10431495 5047229.0 3.0 m 35.0 s 0.5% 10.0 h 10.0 h INFO 06:57:45,815 ProgressMeter - chr1:12984136 5047229.0 3.5 m 41.0 s 0.6% 10.0 h 10.0 h INFO 06:58:15,817 ProgressMeter - chr1:16974204 5047229.0 4.0 m 47.0 s 0.7% 9.4 h 9.3 h INFO 06:58:45,818 ProgressMeter - chr1:19710671 5047229.0 4.5 m 53.0 s 0.8% 9.4 h 9.3 h INFO 06:59:15,821 ProgressMeter - chr1:22909768 5047229.0 5.0 m 59.0 s 0.9% 9.2 h 9.2 h INFO 06:59:45,823 ProgressMeter - chr1:25978820 5047229.0 5.5 m 65.0 s 1.0% 9.2 h 9.1 h INFO 07:00:15,825 ProgressMeter - chr1:32144773 5047229.0 6.0 m 71.0 s 1.2% 8.3 h 8.2 h INFO 07:00:45,833 ProgressMeter - chr1:37985779 5047229.0 6.5 m 77.0 s 1.4% 7.8 h 7.7 h INFO 07:01:15,834 ProgressMeter - chr1:43853738 5047229.0 7.0 m 83.0 s 1.6% 7.4 h 7.3 h INFO 07:01:45,835 ProgressMeter - chr1:52954980 5047229.0 7.5 m 89.0 s 1.9% 6.7 h 6.6 h INFO 07:02:15,837 ProgressMeter - chr1:57758730 5047229.0 8.0 m 95.0 s 2.0% 6.6 h 6.4 h INFO 07:02:45,849 ProgressMeter - chr1:61551296 5047229.0 8.5 m 101.0 s 2.1% 6.6 h 6.5 h INFO 07:03:15,851 ProgressMeter - chr1:65887096 5047229.0 9.0 m 107.0 s 2.3% 6.6 h 6.4 h INFO 07:03:45,852 ProgressMeter - chr1:73395534 5047229.0 9.5 m 112.0 s 2.5% 6.3 h 6.1 h INFO 07:04:15,853 ProgressMeter - chr1:86838255 5047229.0 10.0 m 118.0 s 3.0% 5.6 h 5.5 h INFO 07:04:45,919 ProgressMeter - chr1:93815553 5047229.0 10.5 m 2.1 m 3.2% 5.5 h 5.3 h INFO 07:05:15,922 ProgressMeter - chr1:107003227 5047229.0 11.0 m 2.2 m 3.6% 5.1 h 4.9 h INFO 07:05:45,923 ProgressMeter - chr1:113053167 5047229.0 11.5 m 2.3 m 3.8% 5.0 h 4.8 h INFO 07:06:15,924 ProgressMeter - chr1:116315788 5047229.0 12.0 m 2.4 m 3.9% 5.1 h 4.9 h INFO 07:06:45,925 ProgressMeter - chr1:121125196 5047229.0 12.5 m 2.5 m 4.1% 5.1 h 4.9 h INFO 07:07:25,926 ProgressMeter - chr1:133413886 5047229.0 13.2 m 2.6 m 4.5% 4.9 h 4.7 h INFO 07:07:55,927 ProgressMeter - chr1:145207878 5047229.0 13.7 m 2.7 m 4.8% 4.7 h 4.5 h INFO 07:08:26,827 ProgressMeter - chr1:150648192 5047229.0 14.2 m 2.8 m 5.0% 4.7 h 4.5 h INFO 07:08:56,829 ProgressMeter - chr1:152195115 5047229.0 14.7 m 2.9 m 5.1% 4.8 h 4.6 h INFO 07:09:27,701 ProgressMeter - chr1:154679930 5047229.0 15.2 m 3.0 m 5.2% 4.9 h 4.7 h INFO 07:09:57,707 ProgressMeter - chr1:156608757 5047229.0 15.7 m 3.1 m 5.2% 5.0 h 4.8 h INFO 07:10:27,784 ProgressMeter - chr1:159036184 5047229.0 16.2 m 3.2 m 5.3% 5.1 h 4.8 h INFO 07:10:57,786 ProgressMeter - chr1:160654957 5047229.0 16.7 m 3.3 m 5.3% 5.2 h 4.9 h INFO 07:11:27,788 ProgressMeter - chr1:161631322 5047229.0 17.2 m 3.4 m 5.4% 5.3 h 5.0 h INFO 07:11:57,789 ProgressMeter - chr1:165621970 5047229.0 17.7 m 3.5 m 5.5% 5.4 h 5.1 h INFO 07:12:28,599 ProgressMeter - chr1:169702641 5047229.0 18.2 m 3.6 m 5.6% 5.4 h 5.1 h INFO 07:12:58,600 ProgressMeter - chr1:174884063 5047229.0 18.7 m 3.7 m 5.8% 5.4 h 5.1 h INFO 07:13:28,728 ProgressMeter - chr1:181591644 5047229.0 19.2 m 3.8 m 6.0% 5.3 h 5.0 h INFO 07:13:58,729 ProgressMeter - chr1:185691888 5047229.0 19.7 m 3.9 m 6.2% 5.3 h 5.0 h INFO 07:14:28,730 ProgressMeter - chr1:190410288 5047229.0 20.2 m 4.0 m 6.3% 5.3 h 5.0 h INFO 07:14:59,551 ProgressMeter - chr1:198069859 5047229.0 20.7 m 4.1 m 6.6% 5.3 h 4.9 h INFO 07:15:30,367 ProgressMeter - chr1:201981090 5047229.0 21.2 m 4.2 m 6.7% 5.3 h 4.9 h INFO 07:16:00,368 ProgressMeter - chr1:204806875 5047229.0 21.7 m 4.3 m 6.8% 5.4 h 5.0 h INFO 07:16:31,288 ProgressMeter - chr1:207096794 5047229.0 22.3 m 4.4 m 6.8% 5.4 h 5.0 h INFO 07:17:01,289 ProgressMeter - chr1:209822617 5047229.0 22.8 m 4.5 m 6.9% 5.5 h 5.1 h INFO 07:17:31,290 ProgressMeter - chr1:216475209 5047229.0 23.3 m 4.6 m 7.1% 5.4 h 5.0 h INFO 07:18:02,237 ProgressMeter - chr1:223306470 5047229.0 23.8 m 4.7 m 7.4% 5.4 h 5.0 h INFO 07:18:32,238 ProgressMeter - chr1:228943960 5047229.0 24.3 m 4.8 m 7.5% 5.4 h 5.0 h INFO 07:19:02,478 ProgressMeter - chr1:235933220 5047229.0 24.8 m 4.9 m 7.8% 5.3 h 4.9 h INFO 07:19:42,479 ProgressMeter - chr1:241482232 5047229.0 25.4 m 5.0 m 8.0% 5.3 h 4.9 h INFO 07:20:12,480 ProgressMeter - chr1:248315833 5047229.0 25.9 m 5.1 m 8.2% 5.3 h 4.9 h INFO 07:20:43,613 ProgressMeter - chr2:7726337 2.5429785E8 26.5 m 6.0 s 8.5% 5.2 h 4.8 h INFO 07:21:13,621 ProgressMeter - chr2:17485890 2.5429785E8 27.0 m 6.0 s 8.8% 5.1 h 4.7 h INFO 07:21:53,622 ProgressMeter - chr2:25301371 2.5429785E8 27.6 m 6.0 s 9.0% 5.1 h 4.6 h INFO 07:22:23,623 ProgressMeter - chr2:27237597 2.5429785E8 28.1 m 6.0 s 9.1% 5.2 h 4.7 h INFO 07:22:53,623 ProgressMeter - chr2:28460024 2.5429785E8 28.6 m 6.0 s 9.1% 5.2 h 4.8 h INFO 07:23:23,624 ProgressMeter - chr2:29699092 2.5429785E8 29.1 m 6.0 s 9.2% 5.3 h 4.8 h INFO 07:23:53,625 ProgressMeter - chr2:31641201 2.5429785E8 29.6 m 6.0 s 9.2% 5.4 h 4.9 h INFO 07:24:23,631 ProgressMeter - chr2:33788330 2.5429785E8 30.1 m 7.0 s 9.3% 5.4 h 4.9 h INFO 07:24:53,632 ProgressMeter - chr2:39831224 2.5429785E8 30.6 m 7.0 s 9.5% 5.4 h 4.9 h INFO 07:25:23,633 ProgressMeter - chr2:46392531 2.5429785E8 31.1 m 7.0 s 9.7% 5.3 h 4.8 h INFO 07:25:53,635 ProgressMeter - chr2:58229262 2.5429785E8 31.6 m 7.0 s 10.1% 5.2 h 4.7 h INFO 07:26:23,635 ProgressMeter - chr2:64940967 2.5429785E8 32.1 m 7.0 s 10.3% 5.2 h 4.7 h INFO 07:26:53,636 ProgressMeter - chr2:70679600 2.5429785E8 32.6 m 7.0 s 10.5% 5.2 h 4.6 h INFO 07:27:23,637 ProgressMeter - chr2:80782581 2.5429785E8 33.1 m 7.0 s 10.8% 5.1 h 4.6 h INFO 07:27:53,640 ProgressMeter - chr2:91641488 2.5429785E8 33.6 m 7.0 s 11.2% 5.0 h 4.5 h INFO 07:28:23,642 ProgressMeter - chr2:98697294 2.5429785E8 34.1 m 8.0 s 11.4% 5.0 h 4.4 h INFO 07:28:53,643 ProgressMeter - chr2:102979474 2.5429785E8 34.6 m 8.0 s 11.5% 5.0 h 4.4 h INFO 07:29:23,645 ProgressMeter - chr2:111869188 2.5429785E8 35.1 m 8.0 s 11.8% 5.0 h 4.4 h INFO 07:29:53,646 ProgressMeter - chr2:117526146 2.5429785E8 35.6 m 8.0 s 12.0% 5.0 h 4.4 h INFO 07:30:23,647 ProgressMeter - chr2:128098902 2.5429785E8 36.1 m 8.0 s 12.3% 4.9 h 4.3 h INFO 07:30:53,648 ProgressMeter - chr2:133637059 2.5429785E8 36.6 m 8.0 s 12.5% 4.9 h 4.3 h INFO 07:31:23,657 ProgressMeter - chr2:139606217 2.5429785E8 37.1 m 8.0 s 12.7% 4.9 h 4.3 h INFO 07:32:03,658 ProgressMeter - chr2:156534083 2.5429785E8 37.8 m 8.0 s 13.2% 4.8 h 4.1 h INFO 07:32:33,671 ProgressMeter - chr2:163045250 2.5429785E8 38.3 m 9.0 s 13.5% 4.7 h 4.1 h INFO 07:33:03,672 ProgressMeter - chr2:171331775 2.5429785E8 38.8 m 9.0 s 13.7% 4.7 h 4.1 h INFO 07:33:33,673 ProgressMeter - chr2:177074411 2.5429785E8 39.3 m 9.0 s 13.9% 4.7 h 4.1 h INFO 07:34:03,675 ProgressMeter - chr2:181453207 2.5429785E8 39.8 m 9.0 s 14.1% 4.7 h 4.1 h INFO 07:34:33,676 ProgressMeter - chr2:191745191 2.5429785E8 40.3 m 9.0 s 14.4% 4.7 h 4.0 h INFO 07:35:13,677 ProgressMeter - chr2:201990161 2.5429785E8 41.0 m 9.0 s 14.7% 4.6 h 4.0 h INFO 07:35:43,678 ProgressMeter - chr2:208259627 2.5429785E8 41.5 m 9.0 s 14.9% 4.6 h 3.9 h INFO 07:36:13,725 ProgressMeter - chr2:217789329 2.5429785E8 42.0 m 9.0 s 15.2% 4.6 h 3.9 h INFO 07:36:43,726 ProgressMeter - chr2:226782556 2.5429785E8 42.5 m 10.0 s 15.5% 4.6 h 3.9 h INFO 07:37:13,736 ProgressMeter - chr2:232291503 2.5429785E8 43.0 m 10.0 s 15.7% 4.6 h 3.8 h INFO 07:37:43,738 ProgressMeter - chr2:239638514 2.5429785E8 43.5 m 10.0 s 15.9% 4.5 h 3.8 h INFO 07:38:13,740 ProgressMeter - chr3:1799029 4.97497223E8 44.0 m 5.0 s 16.1% 4.5 h 3.8 h WARN 07:38:42,569 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr3:4872811 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 07:38:43,741 ProgressMeter - chr3:4923738 4.97497223E8 44.5 m 5.0 s 16.2% 4.6 h 3.8 h INFO 07:39:13,741 ProgressMeter - chr3:10284297 4.97497223E8 45.0 m 5.0 s 16.4% 4.6 h 3.8 h INFO 07:39:43,876 ProgressMeter - chr3:15100527 4.97497223E8 45.5 m 5.0 s 16.5% 4.6 h 3.8 h INFO 07:40:13,878 ProgressMeter - chr3:27114463 4.97497223E8 46.0 m 5.0 s 16.9% 4.5 h 3.8 h INFO 07:40:43,879 ProgressMeter - chr3:37146168 4.97497223E8 46.5 m 5.0 s 17.2% 4.5 h 3.7 h INFO 07:41:13,887 ProgressMeter - chr3:42191462 4.97497223E8 47.0 m 5.0 s 17.4% 4.5 h 3.7 h INFO 07:41:43,889 ProgressMeter - chr3:47029599 4.97497223E8 47.5 m 5.0 s 17.6% 4.5 h 3.7 h INFO 07:42:23,890 ProgressMeter - chr3:52366323 4.97497223E8 48.1 m 5.0 s 17.7% 4.5 h 3.7 h INFO 07:42:53,891 ProgressMeter - chr3:55607992 4.97497223E8 48.6 m 5.0 s 17.8% 4.5 h 3.7 h INFO 07:43:23,891 ProgressMeter - chr3:58309455 4.97497223E8 49.1 m 5.0 s 17.9% 4.6 h 3.7 h INFO 07:43:53,892 ProgressMeter - chr3:61726842 4.97497223E8 49.6 m 5.0 s 18.0% 4.6 h 3.8 h INFO 07:44:23,905 ProgressMeter - chr3:65582500 4.97497223E8 50.1 m 6.0 s 18.2% 4.6 h 3.8 h INFO 07:44:53,935 ProgressMeter - chr3:69853561 4.97497223E8 50.6 m 6.0 s 18.3% 4.6 h 3.8 h INFO 07:45:23,936 ProgressMeter - chr3:79567510 4.97497223E8 51.1 m 6.0 s 18.6% 4.6 h 3.7 h INFO 07:45:53,938 ProgressMeter - chr3:93287248 4.97497223E8 51.6 m 6.0 s 19.1% 4.5 h 3.7 h INFO 07:46:23,939 ProgressMeter - chr3:101039836 4.97497223E8 52.1 m 6.0 s 19.3% 4.5 h 3.6 h INFO 07:46:53,940 ProgressMeter - chr3:111491390 4.97497223E8 52.6 m 6.0 s 19.6% 4.5 h 3.6 h INFO 07:47:23,941 ProgressMeter - chr3:120484489 4.97497223E8 53.1 m 6.0 s 19.9% 4.4 h 3.6 h INFO 07:47:53,942 ProgressMeter - chr3:127196321 4.97497223E8 53.6 m 6.0 s 20.1% 4.4 h 3.5 h INFO 07:48:23,944 ProgressMeter - chr3:134075094 4.97497223E8 54.1 m 6.0 s 20.4% 4.4 h 3.5 h INFO 07:48:53,968 ProgressMeter - chr3:141109025 4.97497223E8 54.6 m 6.0 s 20.6% 4.4 h 3.5 h INFO 07:49:23,980 ProgressMeter - chr3:151366517 4.97497223E8 55.1 m 6.0 s 20.9% 4.4 h 3.5 h INFO 07:49:53,982 ProgressMeter - chr3:159546180 4.97497223E8 55.6 m 6.0 s 21.2% 4.4 h 3.4 h INFO 07:50:23,983 ProgressMeter - chr3:172242493 4.97497223E8 56.1 m 6.0 s 21.6% 4.3 h 3.4 h INFO 07:51:03,984 ProgressMeter - chr3:184524350 4.97497223E8 56.8 m 6.0 s 22.0% 4.3 h 3.4 h INFO 07:51:33,991 ProgressMeter - chr3:188157842 4.97497223E8 57.3 m 6.0 s 22.1% 4.3 h 3.4 h INFO 07:52:03,995 ProgressMeter - chr3:193850814 4.97497223E8 57.8 m 6.0 s 22.3% 4.3 h 3.4 h INFO 07:52:34,052 ProgressMeter - chr4:1230151 6.95519653E8 58.3 m 5.0 s 22.5% 4.3 h 3.4 h INFO 07:53:04,053 ProgressMeter - chr4:8279879 6.95519653E8 58.8 m 5.0 s 22.7% 4.3 h 3.3 h INFO 07:53:34,137 ProgressMeter - chr4:15682832 6.95519653E8 59.3 m 5.0 s 22.9% 4.3 h 3.3 h INFO 07:54:04,266 ProgressMeter - chr4:24552949 6.95519653E8 59.8 m 5.0 s 23.2% 4.3 h 3.3 h INFO 07:54:34,267 ProgressMeter - chr4:34539981 6.95519653E8 60.3 m 5.0 s 23.5% 4.3 h 3.3 h INFO 07:55:14,268 ProgressMeter - chr4:42610464 6.95519653E8 61.0 m 5.0 s 23.8% 4.3 h 3.3 h INFO 07:55:44,269 ProgressMeter - chr4:54525870 6.95519653E8 61.5 m 5.0 s 24.2% 4.2 h 3.2 h INFO 07:56:24,270 ProgressMeter - chr4:61528954 6.95519653E8 62.1 m 5.0 s 24.4% 4.2 h 3.2 h INFO 07:57:04,271 ProgressMeter - chr4:74905129 6.95519653E8 62.8 m 5.0 s 24.8% 4.2 h 3.2 h INFO 07:57:34,271 ProgressMeter - chr4:80947133 6.95519653E8 63.3 m 5.0 s 25.0% 4.2 h 3.2 h WARN 07:57:54,975 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr4:87280416 has 12 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 07:58:04,272 ProgressMeter - chr4:88760518 6.95519653E8 63.8 m 5.0 s 25.3% 4.2 h 3.1 h INFO 07:58:34,274 ProgressMeter - chr4:96015670 6.95519653E8 64.3 m 5.0 s 25.5% 4.2 h 3.1 h INFO 07:59:04,275 ProgressMeter - chr4:101133295 6.95519653E8 64.8 m 5.0 s 25.7% 4.2 h 3.1 h INFO 07:59:34,276 ProgressMeter - chr4:108408384 6.95519653E8 65.3 m 5.0 s 25.9% 4.2 h 3.1 h INFO 08:00:04,278 ProgressMeter - chr4:113186156 6.95519653E8 65.8 m 5.0 s 26.1% 4.2 h 3.1 h INFO 08:00:34,278 ProgressMeter - chr4:123379179 6.95519653E8 66.3 m 5.0 s 26.4% 4.2 h 3.1 h INFO 08:01:04,279 ProgressMeter - chr4:136651872 6.95519653E8 66.8 m 5.0 s 26.8% 4.1 h 3.0 h INFO 08:01:34,286 ProgressMeter - chr4:145146675 6.95519653E8 67.3 m 5.0 s 27.1% 4.1 h 3.0 h INFO 08:02:04,300 ProgressMeter - chr4:155544417 6.95519653E8 67.8 m 5.0 s 27.4% 4.1 h 3.0 h INFO 08:02:34,301 ProgressMeter - chr4:169184152 6.95519653E8 68.3 m 5.0 s 27.9% 4.1 h 2.9 h INFO 08:03:04,348 ProgressMeter - chr4:180596905 6.95519653E8 68.8 m 5.0 s 28.3% 4.1 h 2.9 h INFO 08:03:34,349 ProgressMeter - chr4:187126564 6.95519653E8 69.3 m 5.0 s 28.5% 4.1 h 2.9 h INFO 08:04:04,350 ProgressMeter - chr5:1847223 8.86673929E8 69.8 m 4.0 s 28.7% 4.1 h 2.9 h INFO 08:04:34,352 ProgressMeter - chr5:11787349 8.86673929E8 70.3 m 4.0 s 29.0% 4.0 h 2.9 h INFO 08:05:04,353 ProgressMeter - chr5:26641177 8.86673929E8 70.8 m 4.0 s 29.5% 4.0 h 2.8 h INFO 08:05:34,355 ProgressMeter - chr5:35233925 8.86673929E8 71.3 m 4.0 s 29.7% 4.0 h 2.8 h INFO 08:06:04,357 ProgressMeter - chr5:39306857 8.86673929E8 71.8 m 4.0 s 29.9% 4.0 h 2.8 h INFO 08:06:34,358 ProgressMeter - chr5:44390810 8.86673929E8 72.3 m 4.0 s 30.0% 4.0 h 2.8 h INFO 08:07:04,359 ProgressMeter - chr5:55355371 8.86673929E8 72.8 m 4.0 s 30.4% 4.0 h 2.8 h INFO 08:07:34,360 ProgressMeter - chr5:66480271 8.86673929E8 73.3 m 4.0 s 30.7% 4.0 h 2.8 h INFO 08:08:04,361 ProgressMeter - chr5:75129801 8.86673929E8 73.8 m 4.0 s 31.0% 4.0 h 2.7 h INFO 08:08:44,362 ProgressMeter - chr5:86668214 8.86673929E8 74.5 m 5.0 s 31.4% 4.0 h 2.7 h INFO 08:09:14,363 ProgressMeter - chr5:96470914 8.86673929E8 75.0 m 5.0 s 31.7% 3.9 h 2.7 h INFO 08:09:44,364 ProgressMeter - chr5:110284082 8.86673929E8 75.5 m 5.0 s 32.2% 3.9 h 2.7 h INFO 08:10:14,365 ProgressMeter - chr5:120162684 8.86673929E8 76.0 m 5.0 s 32.5% 3.9 h 2.6 h INFO 08:10:44,366 ProgressMeter - chr5:131877469 8.86673929E8 76.5 m 5.0 s 32.8% 3.9 h 2.6 h INFO 08:11:14,368 ProgressMeter - chr5:137558329 8.86673929E8 77.0 m 5.0 s 33.0% 3.9 h 2.6 h INFO 08:11:44,375 ProgressMeter - chr5:140913972 8.86673929E8 77.5 m 5.0 s 33.1% 3.9 h 2.6 h INFO 08:12:14,376 ProgressMeter - chr5:147548220 8.86673929E8 78.0 m 5.0 s 33.4% 3.9 h 2.6 h INFO 08:12:44,377 ProgressMeter - chr5:150560988 8.86673929E8 78.5 m 5.0 s 33.5% 3.9 h 2.6 h INFO 08:13:14,378 ProgressMeter - chr5:156579245 8.86673929E8 79.0 m 5.0 s 33.6% 3.9 h 2.6 h INFO 08:13:44,379 ProgressMeter - chr5:160785370 8.86673929E8 79.5 m 5.0 s 33.8% 3.9 h 2.6 h INFO 08:14:14,380 ProgressMeter - chr5:170850811 8.86673929E8 80.0 m 5.0 s 34.1% 3.9 h 2.6 h INFO 08:14:44,381 ProgressMeter - chr5:177270865 8.86673929E8 80.5 m 5.0 s 34.3% 3.9 h 2.6 h INFO 08:15:14,382 ProgressMeter - chr6:348094 1.067589189E9 81.0 m 4.0 s 34.4% 3.9 h 2.6 h INFO 08:15:44,383 ProgressMeter - chr6:8565689 1.067589189E9 81.5 m 4.0 s 34.7% 3.9 h 2.6 h INFO 08:16:14,384 ProgressMeter - chr6:17013734 1.067589189E9 82.0 m 4.0 s 35.0% 3.9 h 2.5 h INFO 08:16:44,385 ProgressMeter - chr6:22721897 1.067589189E9 82.5 m 4.0 s 35.2% 3.9 h 2.5 h INFO 08:17:14,386 ProgressMeter - chr6:31326877 1.067589189E9 83.0 m 4.0 s 35.4% 3.9 h 2.5 h INFO 08:17:44,387 ProgressMeter - chr6:32551762 1.067589189E9 83.5 m 4.0 s 35.5% 3.9 h 2.5 h INFO 08:18:14,389 ProgressMeter - chr6:33505732 1.067589189E9 84.0 m 4.0 s 35.5% 3.9 h 2.5 h INFO 08:18:44,390 ProgressMeter - chr6:37077948 1.067589189E9 84.5 m 4.0 s 35.6% 4.0 h 2.5 h INFO 08:19:14,391 ProgressMeter - chr6:43058325 1.067589189E9 85.0 m 4.0 s 35.8% 4.0 h 2.5 h INFO 08:19:44,392 ProgressMeter - chr6:50216210 1.067589189E9 85.5 m 4.0 s 36.0% 4.0 h 2.5 h INFO 08:20:14,394 ProgressMeter - chr6:56037538 1.067589189E9 86.0 m 4.0 s 36.2% 4.0 h 2.5 h INFO 08:20:44,409 ProgressMeter - chr6:72031083 1.067589189E9 86.5 m 4.0 s 36.8% 3.9 h 2.5 h INFO 08:21:24,410 ProgressMeter - chr6:86768149 1.067589189E9 87.1 m 4.0 s 37.2% 3.9 h 2.4 h INFO 08:21:54,417 ProgressMeter - chr6:94903455 1.067589189E9 87.6 m 4.0 s 37.5% 3.9 h 2.4 h INFO 08:22:24,498 ProgressMeter - chr6:106546890 1.067589189E9 88.1 m 4.0 s 37.9% 3.9 h 2.4 h INFO 08:22:54,499 ProgressMeter - chr6:112072687 1.067589189E9 88.6 m 4.0 s 38.0% 3.9 h 2.4 h INFO 08:23:24,501 ProgressMeter - chr6:122161500 1.067589189E9 89.1 m 5.0 s 38.4% 3.9 h 2.4 h INFO 08:23:54,502 ProgressMeter - chr6:128858418 1.067589189E9 89.6 m 5.0 s 38.6% 3.9 h 2.4 h INFO 08:24:24,503 ProgressMeter - chr6:137322034 1.067589189E9 90.1 m 5.0 s 38.9% 3.9 h 2.4 h INFO 08:24:54,505 ProgressMeter - chr6:145851264 1.067589189E9 90.6 m 5.0 s 39.1% 3.9 h 2.3 h INFO 08:25:24,507 ProgressMeter - chr6:153316884 1.067589189E9 91.1 m 5.0 s 39.4% 3.9 h 2.3 h INFO 08:26:04,508 ProgressMeter - chr6:161478415 1.067589189E9 91.8 m 5.0 s 39.6% 3.9 h 2.3 h INFO 08:26:34,509 ProgressMeter - chr6:168297758 1.067589189E9 92.3 m 5.0 s 39.9% 3.9 h 2.3 h INFO 08:27:04,511 ProgressMeter - chr7:2274694 1.238704256E9 92.8 m 4.0 s 40.0% 3.9 h 2.3 h INFO 08:27:34,513 ProgressMeter - chr7:9060359 1.238704256E9 93.3 m 4.0 s 40.2% 3.9 h 2.3 h INFO 08:28:04,514 ProgressMeter - chr7:17360240 1.238704256E9 93.8 m 4.0 s 40.5% 3.9 h 2.3 h INFO 08:28:34,515 ProgressMeter - chr7:22331218 1.238704256E9 94.3 m 4.0 s 40.7% 3.9 h 2.3 h INFO 08:29:04,516 ProgressMeter - chr7:28648788 1.238704256E9 94.8 m 4.0 s 40.9% 3.9 h 2.3 h INFO 08:29:34,517 ProgressMeter - chr7:37270451 1.238704256E9 95.3 m 4.0 s 41.2% 3.9 h 2.3 h INFO 08:30:04,522 ProgressMeter - chr7:44351891 1.238704256E9 95.8 m 4.0 s 41.4% 3.9 h 2.3 h INFO 08:30:34,523 ProgressMeter - chr7:52868232 1.238704256E9 96.3 m 4.0 s 41.7% 3.9 h 2.2 h INFO 08:31:04,524 ProgressMeter - chr7:63894921 1.238704256E9 96.8 m 4.0 s 42.0% 3.8 h 2.2 h INFO 08:31:34,525 ProgressMeter - chr7:73623349 1.238704256E9 97.3 m 4.0 s 42.3% 3.8 h 2.2 h INFO 08:32:04,533 ProgressMeter - chr7:80270258 1.238704256E9 97.8 m 4.0 s 42.5% 3.8 h 2.2 h INFO 08:32:34,534 ProgressMeter - chr7:90560305 1.238704256E9 98.3 m 4.0 s 42.9% 3.8 h 2.2 h INFO 08:33:04,534 ProgressMeter - chr7:96557143 1.238704256E9 98.8 m 4.0 s 43.1% 3.8 h 2.2 h INFO 08:33:34,536 ProgressMeter - chr7:101047232 1.238704256E9 99.3 m 4.0 s 43.2% 3.8 h 2.2 h INFO 08:34:04,537 ProgressMeter - chr7:107110408 1.238704256E9 99.8 m 4.0 s 43.4% 3.8 h 2.2 h INFO 08:34:34,539 ProgressMeter - chr7:115929538 1.238704256E9 100.3 m 4.0 s 43.7% 3.8 h 2.2 h INFO 08:35:04,540 ProgressMeter - chr7:123298229 1.238704256E9 100.8 m 4.0 s 43.9% 3.8 h 2.1 h INFO 08:35:34,541 ProgressMeter - chr7:130460716 1.238704256E9 101.3 m 4.0 s 44.2% 3.8 h 2.1 h INFO 08:36:04,542 ProgressMeter - chr7:138095665 1.238704256E9 101.8 m 4.0 s 44.4% 3.8 h 2.1 h INFO 08:36:34,545 ProgressMeter - chr7:142144116 1.238704256E9 102.3 m 4.0 s 44.5% 3.8 h 2.1 h INFO 08:37:04,546 ProgressMeter - chr7:148036714 1.238704256E9 102.8 m 4.0 s 44.7% 3.8 h 2.1 h INFO 08:37:34,547 ProgressMeter - chr7:155104463 1.238704256E9 103.3 m 5.0 s 45.0% 3.8 h 2.1 h INFO 08:38:04,548 ProgressMeter - chr8:1855884 1.397842919E9 103.8 m 4.0 s 45.1% 3.8 h 2.1 h INFO 08:38:34,550 ProgressMeter - chr8:6369661 1.397842919E9 104.3 m 4.0 s 45.3% 3.8 h 2.1 h INFO 08:39:04,552 ProgressMeter - chr8:11422789 1.397842919E9 104.8 m 4.0 s 45.4% 3.8 h 2.1 h INFO 08:39:34,553 ProgressMeter - chr8:20770843 1.397842919E9 105.3 m 4.0 s 45.8% 3.8 h 2.1 h INFO 08:40:04,643 ProgressMeter - chr8:27346898 1.397842919E9 105.8 m 4.0 s 46.0% 3.8 h 2.1 h INFO 08:40:34,644 ProgressMeter - chr8:32997228 1.397842919E9 106.3 m 4.0 s 46.1% 3.8 h 2.1 h INFO 08:41:04,646 ProgressMeter - chr8:41413631 1.397842919E9 106.8 m 4.0 s 46.4% 3.8 h 2.1 h INFO 08:41:34,648 ProgressMeter - chr8:52569595 1.397842919E9 107.3 m 4.0 s 46.8% 3.8 h 2.0 h INFO 08:42:04,655 ProgressMeter - chr8:65797487 1.397842919E9 107.8 m 4.0 s 47.2% 3.8 h 2.0 h INFO 08:42:34,657 ProgressMeter - chr8:79496643 1.397842919E9 108.3 m 4.0 s 47.6% 3.8 h 119.0 m INFO 08:43:04,659 ProgressMeter - chr8:90782493 1.397842919E9 108.8 m 4.0 s 48.0% 3.8 h 117.8 m INFO 08:43:34,661 ProgressMeter - chr8:101765897 1.397842919E9 109.3 m 4.0 s 48.4% 3.8 h 116.7 m INFO 08:44:04,662 ProgressMeter - chr8:111593538 1.397842919E9 109.8 m 4.0 s 48.7% 3.8 h 115.8 m INFO 08:44:34,663 ProgressMeter - chr8:124520778 1.397842919E9 110.3 m 4.0 s 49.1% 3.7 h 114.4 m INFO 08:45:04,665 ProgressMeter - chr8:131012226 1.397842919E9 110.8 m 4.0 s 49.3% 3.7 h 113.9 m INFO 08:45:34,666 ProgressMeter - chr8:135611780 1.397842919E9 111.3 m 4.0 s 49.5% 3.8 h 113.8 m INFO 08:46:04,667 ProgressMeter - chr8:143737499 1.397842919E9 111.8 m 4.0 s 49.7% 3.7 h 113.1 m INFO 08:46:34,668 ProgressMeter - chr9:3862472 1.544206941E9 112.3 m 4.0 s 49.9% 3.7 h 112.6 m INFO 08:47:04,669 ProgressMeter - chr9:5968740 1.544206941E9 112.8 m 4.0 s 50.0% 3.8 h 112.8 m INFO 08:47:34,672 ProgressMeter - chr9:16020153 1.544206941E9 113.3 m 4.0 s 50.3% 3.8 h 111.9 m INFO 08:48:04,673 ProgressMeter - chr9:17302438 1.544206941E9 113.8 m 4.0 s 50.4% 3.8 h 112.2 m INFO 08:48:34,674 ProgressMeter - chr9:20941672 1.544206941E9 114.3 m 4.0 s 50.5% 3.8 h 112.1 m INFO 08:49:04,674 ProgressMeter - chr9:22536609 1.544206941E9 114.8 m 4.0 s 50.5% 3.8 h 112.4 m INFO 08:49:34,675 ProgressMeter - chr9:32432294 1.544206941E9 115.3 m 4.0 s 50.8% 3.8 h 111.5 m INFO 08:50:04,677 ProgressMeter - chr9:35698209 1.544206941E9 115.8 m 4.0 s 51.0% 3.8 h 111.5 m INFO 08:50:34,678 ProgressMeter - chr9:43163380 1.544206941E9 116.3 m 4.0 s 51.2% 3.8 h 110.9 m INFO 08:51:05,112 ProgressMeter - chr9:67154308 1.544206941E9 116.8 m 4.0 s 52.0% 3.7 h 108.0 m INFO 08:51:35,383 ProgressMeter - chr9:77772258 1.544206941E9 117.3 m 4.0 s 52.3% 3.7 h 107.0 m INFO 08:52:05,390 ProgressMeter - chr9:86590307 1.544206941E9 117.8 m 4.0 s 52.6% 3.7 h 106.2 m INFO 08:52:35,476 ProgressMeter - chr9:96019482 1.544206941E9 118.3 m 4.0 s 52.9% 3.7 h 105.4 m INFO 08:53:05,478 ProgressMeter - chr9:101259152 1.544206941E9 118.8 m 4.0 s 53.1% 3.7 h 105.1 m INFO 08:53:35,479 ProgressMeter - chr9:108079308 1.544206941E9 119.3 m 4.0 s 53.3% 3.7 h 104.6 m INFO 08:54:05,481 ProgressMeter - chr9:114888508 1.544206941E9 119.8 m 4.0 s 53.5% 3.7 h 104.1 m INFO 08:54:35,482 ProgressMeter - chr9:120466277 1.544206941E9 2.0 h 4.0 s 53.7% 3.7 h 103.8 m INFO 08:55:05,483 ProgressMeter - chr9:124062991 1.544206941E9 2.0 h 4.0 s 53.8% 3.7 h 103.7 m INFO 08:55:35,484 ProgressMeter - chr9:130565958 1.544206941E9 2.0 h 4.0 s 54.0% 3.7 h 103.3 m INFO 08:56:05,485 ProgressMeter - chr9:134495970 1.544206941E9 2.0 h 4.0 s 54.1% 3.8 h 103.2 m INFO 08:56:35,487 ProgressMeter - chr9:136657775 1.544206941E9 2.0 h 4.0 s 54.2% 3.8 h 103.3 m INFO 08:57:15,488 ProgressMeter - chr10:1657501 1.685420372E9 2.0 h 4.0 s 54.4% 3.8 h 103.1 m INFO 08:57:45,489 ProgressMeter - chr10:7303131 1.685420372E9 2.1 h 4.0 s 54.6% 3.8 h 102.7 m INFO 08:58:25,490 ProgressMeter - chr10:14996088 1.685420372E9 2.1 h 4.0 s 54.8% 3.8 h 102.2 m INFO 08:59:05,491 ProgressMeter - chr10:25762812 1.685420372E9 2.1 h 4.0 s 55.2% 3.8 h 101.4 m INFO 08:59:35,634 ProgressMeter - chr10:31586483 1.685420372E9 2.1 h 4.0 s 55.4% 3.8 h 101.0 m INFO 09:00:05,636 ProgressMeter - chr10:37726898 1.685420372E9 2.1 h 4.0 s 55.6% 3.8 h 100.6 m INFO 09:00:45,637 ProgressMeter - chr10:45468687 1.685420372E9 2.1 h 4.0 s 55.8% 3.8 h 100.1 m INFO 09:01:15,638 ProgressMeter - chr10:50141509 1.685420372E9 2.1 h 4.0 s 56.0% 3.8 h 99.9 m INFO 09:01:45,640 ProgressMeter - chr10:54994747 1.685420372E9 2.1 h 4.0 s 56.1% 3.8 h 99.6 m INFO 09:02:15,642 ProgressMeter - chr10:64281388 1.685420372E9 2.1 h 4.0 s 56.4% 3.8 h 98.8 m INFO 09:02:45,897 ProgressMeter - chr10:72059286 1.685420372E9 2.1 h 4.0 s 56.7% 3.8 h 98.2 m INFO 09:03:15,899 ProgressMeter - chr10:75962005 1.685420372E9 2.2 h 4.0 s 56.8% 3.8 h 98.1 m INFO 09:03:45,900 ProgressMeter - chr10:82263170 1.685420372E9 2.2 h 4.0 s 57.0% 3.8 h 97.7 m INFO 09:04:15,901 ProgressMeter - chr10:89631722 1.685420372E9 2.2 h 4.0 s 57.2% 3.8 h 97.1 m INFO 09:04:45,974 ProgressMeter - chr10:95347102 1.685420372E9 2.2 h 4.0 s 57.4% 3.8 h 96.7 m INFO 09:05:15,977 ProgressMeter - chr10:99192973 1.685420372E9 2.2 h 4.0 s 57.6% 3.8 h 96.6 m INFO 09:05:45,978 ProgressMeter - chr10:102407057 1.685420372E9 2.2 h 4.0 s 57.7% 3.8 h 96.6 m WARN 09:05:52,384 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr10:103202019 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 09:06:26,220 ProgressMeter - chr10:105837363 1.685420372E9 2.2 h 4.0 s 57.8% 3.8 h 96.6 m INFO 09:06:56,227 ProgressMeter - chr10:115331713 1.685420372E9 2.2 h 4.0 s 58.1% 3.8 h 95.8 m INFO 09:07:26,229 ProgressMeter - chr10:121014533 1.685420372E9 2.2 h 4.0 s 58.3% 3.8 h 95.4 m INFO 09:07:56,230 ProgressMeter - chr10:129132159 1.685420372E9 2.2 h 4.0 s 58.5% 3.8 h 94.7 m INFO 09:08:26,573 ProgressMeter - chr11:244415 1.820955119E9 2.2 h 4.0 s 58.7% 3.8 h 94.3 m INFO 09:08:56,578 ProgressMeter - chr11:5043764 1.820955119E9 2.2 h 4.0 s 58.9% 3.8 h 94.0 m INFO 09:09:26,579 ProgressMeter - chr11:12204893 1.820955119E9 2.3 h 4.0 s 59.1% 3.8 h 93.5 m INFO 09:09:56,592 ProgressMeter - chr11:17123510 1.820955119E9 2.3 h 4.0 s 59.3% 3.8 h 93.2 m INFO 09:10:26,593 ProgressMeter - chr11:20312414 1.820955119E9 2.3 h 4.0 s 59.4% 3.8 h 93.1 m INFO 09:10:56,596 ProgressMeter - chr11:27601562 1.820955119E9 2.3 h 4.0 s 59.6% 3.8 h 92.6 m INFO 09:11:26,597 ProgressMeter - chr11:35266301 1.820955119E9 2.3 h 4.0 s 59.9% 3.8 h 92.0 m INFO 09:11:56,599 ProgressMeter - chr11:45509751 1.820955119E9 2.3 h 4.0 s 60.2% 3.8 h 91.0 m INFO 09:12:26,608 ProgressMeter - chr11:55259358 1.820955119E9 2.3 h 4.0 s 60.5% 3.8 h 90.2 m INFO 09:12:56,609 ProgressMeter - chr11:60740535 1.820955119E9 2.3 h 4.0 s 60.7% 3.8 h 89.8 m INFO 09:13:26,611 ProgressMeter - chr11:64645482 1.820955119E9 2.3 h 4.0 s 60.8% 3.8 h 89.7 m INFO 09:13:56,612 ProgressMeter - chr11:67039663 1.820955119E9 2.3 h 4.0 s 60.9% 3.8 h 89.7 m INFO 09:14:26,614 ProgressMeter - chr11:71708237 1.820955119E9 2.3 h 4.0 s 61.0% 3.8 h 89.5 m INFO 09:15:06,615 ProgressMeter - chr11:80953351 1.820955119E9 2.3 h 4.0 s 61.3% 3.8 h 88.8 m INFO 09:15:36,617 ProgressMeter - chr11:93084882 1.820955119E9 2.4 h 4.0 s 61.7% 3.8 h 87.6 m INFO 09:16:06,619 ProgressMeter - chr11:103510455 1.820955119E9 2.4 h 4.0 s 62.1% 3.8 h 86.7 m INFO 09:16:36,620 ProgressMeter - chr11:111531863 1.820955119E9 2.4 h 4.0 s 62.3% 3.8 h 86.0 m INFO 09:17:06,622 ProgressMeter - chr11:118135070 1.820955119E9 2.4 h 4.0 s 62.5% 3.8 h 85.6 m INFO 09:17:36,630 ProgressMeter - chr11:120350756 1.820955119E9 2.4 h 4.0 s 62.6% 3.8 h 85.6 m INFO 09:18:06,632 ProgressMeter - chr11:130590226 1.820955119E9 2.4 h 4.0 s 62.9% 3.8 h 84.7 m INFO 09:18:36,654 ProgressMeter - chr12:3077607 1.955961635E9 2.4 h 4.0 s 63.2% 3.8 h 84.1 m INFO 09:19:06,656 ProgressMeter - chr12:6966103 1.955961635E9 2.4 h 4.0 s 63.3% 3.8 h 84.0 m INFO 09:19:36,657 ProgressMeter - chr12:9587124 1.955961635E9 2.4 h 4.0 s 63.4% 3.8 h 83.9 m INFO 09:20:06,658 ProgressMeter - chr12:13539611 1.955961635E9 2.4 h 4.0 s 63.5% 3.8 h 83.8 m INFO 09:20:36,659 ProgressMeter - chr12:21067247 1.955961635E9 2.4 h 4.0 s 63.8% 3.8 h 83.2 m INFO 09:21:06,671 ProgressMeter - chr12:31242596 1.955961635E9 2.4 h 4.0 s 64.1% 3.8 h 82.3 m INFO 09:21:36,673 ProgressMeter - chr12:39119294 1.955961635E9 2.5 h 4.0 s 64.3% 3.8 h 81.7 m INFO 09:22:06,674 ProgressMeter - chr12:43316538 1.955961635E9 2.5 h 4.0 s 64.5% 3.8 h 81.4 m INFO 09:22:36,742 ProgressMeter - chr12:49181392 1.955961635E9 2.5 h 4.0 s 64.7% 3.8 h 81.0 m INFO 09:23:06,745 ProgressMeter - chr12:52571344 1.955961635E9 2.5 h 4.0 s 64.8% 3.8 h 80.9 m INFO 09:23:36,746 ProgressMeter - chr12:56335470 1.955961635E9 2.5 h 4.0 s 64.9% 3.8 h 80.8 m INFO 09:24:06,746 ProgressMeter - chr12:57674336 1.955961635E9 2.5 h 4.0 s 64.9% 3.8 h 80.9 m INFO 09:24:36,748 ProgressMeter - chr12:64818961 1.955961635E9 2.5 h 4.0 s 65.2% 3.8 h 80.3 m INFO 09:25:06,750 ProgressMeter - chr12:72083249 1.955961635E9 2.5 h 4.0 s 65.4% 3.8 h 79.8 m INFO 09:25:36,751 ProgressMeter - chr12:79609076 1.955961635E9 2.5 h 4.0 s 65.6% 3.8 h 79.2 m INFO 09:26:06,753 ProgressMeter - chr12:93219782 1.955961635E9 2.5 h 4.0 s 66.1% 3.8 h 77.9 m INFO 09:26:36,754 ProgressMeter - chr12:99761783 1.955961635E9 2.5 h 4.0 s 66.3% 3.8 h 77.4 m INFO 09:27:06,775 ProgressMeter - chr12:105418916 1.955961635E9 2.5 h 4.0 s 66.5% 3.8 h 77.1 m INFO 09:27:36,776 ProgressMeter - chr12:111169875 1.955961635E9 2.6 h 4.0 s 66.7% 3.8 h 76.7 m INFO 09:28:06,778 ProgressMeter - chr12:117876959 1.955961635E9 2.6 h 4.0 s 66.9% 3.8 h 76.2 m INFO 09:28:36,779 ProgressMeter - chr12:123719807 1.955961635E9 2.6 h 4.0 s 67.1% 3.8 h 75.8 m INFO 09:29:06,795 ProgressMeter - chr12:131562075 1.955961635E9 2.6 h 4.0 s 67.3% 3.8 h 75.2 m INFO 09:29:36,964 ProgressMeter - chr13:17880401 2.08981353E9 2.6 h 4.0 s 68.0% 3.8 h 73.2 m INFO 09:30:06,965 ProgressMeter - chr13:24876897 2.08981353E9 2.6 h 4.0 s 68.2% 3.8 h 72.7 m INFO 09:30:36,966 ProgressMeter - chr13:30431969 2.08981353E9 2.6 h 4.0 s 68.4% 3.8 h 72.3 m INFO 09:31:06,967 ProgressMeter - chr13:37155555 2.08981353E9 2.6 h 4.0 s 68.6% 3.8 h 71.8 m INFO 09:31:46,968 ProgressMeter - chr13:47840748 2.08981353E9 2.6 h 4.0 s 68.9% 3.8 h 71.0 m INFO 09:32:16,969 ProgressMeter - chr13:58160648 2.08981353E9 2.6 h 4.0 s 69.3% 3.8 h 70.1 m INFO 09:32:46,976 ProgressMeter - chr13:74482091 2.08981353E9 2.6 h 4.0 s 69.8% 3.8 h 68.6 m INFO 09:33:16,977 ProgressMeter - chr13:84346406 2.08981353E9 2.7 h 4.0 s 70.1% 3.8 h 67.8 m INFO 09:33:46,978 ProgressMeter - chr13:93546757 2.08981353E9 2.7 h 4.0 s 70.4% 3.8 h 67.0 m INFO 09:34:16,979 ProgressMeter - chr13:106890175 2.08981353E9 2.7 h 4.0 s 70.8% 3.8 h 65.9 m INFO 09:34:46,981 ProgressMeter - chr13:114877454 2.08981353E9 2.7 h 4.0 s 71.1% 3.8 h 65.2 m INFO 09:35:16,992 ProgressMeter - chr14:20846199 2.204983408E9 2.7 h 4.0 s 71.8% 3.7 h 63.3 m INFO 09:35:46,994 ProgressMeter - chr14:22979711 2.204983408E9 2.7 h 4.0 s 71.9% 3.7 h 63.3 m INFO 09:36:16,995 ProgressMeter - chr14:24554491 2.204983408E9 2.7 h 4.0 s 71.9% 3.8 h 63.3 m INFO 09:36:46,997 ProgressMeter - chr14:34189030 2.204983408E9 2.7 h 4.0 s 72.2% 3.8 h 62.5 m INFO 09:37:16,999 ProgressMeter - chr14:47509957 2.204983408E9 2.7 h 4.0 s 72.6% 3.7 h 61.4 m INFO 09:37:47,002 ProgressMeter - chr14:57971883 2.204983408E9 2.7 h 4.0 s 73.0% 3.7 h 60.5 m INFO 09:38:17,003 ProgressMeter - chr14:64931810 2.204983408E9 2.7 h 4.0 s 73.2% 3.7 h 60.0 m INFO 09:38:47,005 ProgressMeter - chr14:68773907 2.204983408E9 2.7 h 4.0 s 73.3% 3.7 h 59.8 m INFO 09:39:17,007 ProgressMeter - chr14:73291988 2.204983408E9 2.8 h 4.0 s 73.5% 3.7 h 59.6 m INFO 09:39:47,008 ProgressMeter - chr14:78997010 2.204983408E9 2.8 h 4.0 s 73.7% 3.7 h 59.2 m INFO 09:40:17,009 ProgressMeter - chr14:88451153 2.204983408E9 2.8 h 4.0 s 74.0% 3.7 h 58.4 m INFO 09:40:47,011 ProgressMeter - chr14:97214915 2.204983408E9 2.8 h 4.0 s 74.2% 3.7 h 57.8 m INFO 09:41:17,013 ProgressMeter - chr14:103116286 2.204983408E9 2.8 h 4.0 s 74.4% 3.7 h 57.4 m INFO 09:41:47,015 ProgressMeter - chr15:2763100 2.312332948E9 2.8 h 4.0 s 74.7% 3.7 h 56.8 m INFO 09:42:17,017 ProgressMeter - chr15:21935557 2.312332948E9 2.8 h 4.0 s 75.3% 3.7 h 55.2 m INFO 09:42:47,018 ProgressMeter - chr15:29133246 2.312332948E9 2.8 h 4.0 s 75.5% 3.7 h 54.6 m INFO 09:43:17,361 ProgressMeter - chr15:38065026 2.312332948E9 2.8 h 4.0 s 75.8% 3.7 h 54.0 m WARN 09:43:32,038 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr15:40582128 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 09:43:47,363 ProgressMeter - chr15:42039474 2.312332948E9 2.8 h 4.0 s 75.9% 3.7 h 53.7 m INFO 09:44:17,364 ProgressMeter - chr15:49777469 2.312332948E9 2.8 h 4.0 s 76.2% 3.7 h 53.2 m INFO 09:44:47,366 ProgressMeter - chr15:54811865 2.312332948E9 2.8 h 4.0 s 76.3% 3.7 h 52.8 m INFO 09:45:17,368 ProgressMeter - chr15:60643665 2.312332948E9 2.9 h 4.0 s 76.5% 3.7 h 52.4 m INFO 09:45:47,369 ProgressMeter - chr15:61400164 2.312332948E9 2.9 h 4.0 s 76.6% 3.7 h 52.5 m INFO 09:46:17,371 ProgressMeter - chr15:66773728 2.312332948E9 2.9 h 4.0 s 76.7% 3.7 h 52.2 m INFO 09:46:47,372 ProgressMeter - chr15:74549863 2.312332948E9 2.9 h 4.0 s 77.0% 3.7 h 51.6 m INFO 09:47:17,374 ProgressMeter - chr15:78165069 2.312332948E9 2.9 h 4.0 s 77.1% 3.7 h 51.4 m INFO 09:47:47,375 ProgressMeter - chr15:83677741 2.312332948E9 2.9 h 4.0 s 77.3% 3.7 h 51.0 m INFO 09:48:17,376 ProgressMeter - chr15:91026049 2.312332948E9 2.9 h 4.0 s 77.5% 3.7 h 50.5 m INFO 09:48:47,377 ProgressMeter - chr15:100963980 2.312332948E9 2.9 h 4.0 s 77.8% 3.7 h 49.7 m INFO 09:49:17,379 ProgressMeter - chr16:3274903 2.41486434E9 2.9 h 4.0 s 78.0% 3.7 h 49.4 m INFO 09:49:47,429 ProgressMeter - chr16:10148114 2.41486434E9 2.9 h 4.0 s 78.2% 3.7 h 48.9 m INFO 09:50:17,439 ProgressMeter - chr16:13809336 2.41486434E9 2.9 h 4.0 s 78.3% 3.7 h 48.7 m INFO 09:50:47,676 ProgressMeter - chr16:22917310 2.41486434E9 2.9 h 4.0 s 78.6% 3.7 h 48.0 m INFO 09:51:17,677 ProgressMeter - chr16:27376231 2.41486434E9 3.0 h 4.0 s 78.8% 3.7 h 47.7 m INFO 09:51:48,081 ProgressMeter - chr16:30615526 2.41486434E9 3.0 h 4.0 s 78.9% 3.8 h 47.6 m INFO 09:52:18,310 ProgressMeter - chr16:34325822 2.41486434E9 3.0 h 4.0 s 79.0% 3.8 h 47.4 m INFO 09:52:48,311 ProgressMeter - chr16:49548034 2.41486434E9 3.0 h 4.0 s 79.5% 3.7 h 46.1 m INFO 09:53:18,313 ProgressMeter - chr16:56919297 2.41486434E9 3.0 h 4.0 s 79.7% 3.7 h 45.6 m INFO 09:53:48,315 ProgressMeter - chr16:67160851 2.41486434E9 3.0 h 4.0 s 80.0% 3.7 h 44.8 m INFO 09:54:18,318 ProgressMeter - chr16:69500757 2.41486434E9 3.0 h 4.0 s 80.1% 3.7 h 44.7 m INFO 09:54:48,321 ProgressMeter - chr16:72987555 2.41486434E9 3.0 h 4.0 s 80.2% 3.8 h 44.5 m INFO 09:55:18,323 ProgressMeter - chr16:79693457 2.41486434E9 3.0 h 4.0 s 80.5% 3.8 h 44.0 m INFO 09:55:48,325 ProgressMeter - chr16:86236407 2.41486434E9 3.0 h 4.0 s 80.7% 3.8 h 43.5 m INFO 09:56:18,326 ProgressMeter - chr17:2324893 2.505219093E9 3.0 h 4.0 s 80.9% 3.8 h 43.1 m INFO 09:56:48,327 ProgressMeter - chr17:5308966 2.505219093E9 3.0 h 4.0 s 81.0% 3.8 h 42.9 m INFO 09:57:18,330 ProgressMeter - chr17:9353695 2.505219093E9 3.1 h 4.0 s 81.1% 3.8 h 42.7 m INFO 09:57:48,331 ProgressMeter - chr17:18598337 2.505219093E9 3.1 h 4.0 s 81.4% 3.8 h 42.0 m INFO 09:58:18,332 ProgressMeter - chr17:21218381 2.505219093E9 3.1 h 4.0 s 81.5% 3.8 h 41.8 m INFO 09:58:48,335 ProgressMeter - chr17:21310725 2.505219093E9 3.1 h 4.0 s 81.5% 3.8 h 41.9 m INFO 09:59:18,336 ProgressMeter - chr17:29667292 2.505219093E9 3.1 h 4.0 s 81.8% 3.8 h 41.3 m WARN 09:59:34,744 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr17:33593196 has 11 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 09:59:48,338 ProgressMeter - chr17:35879274 2.505219093E9 3.1 h 4.0 s 82.0% 3.8 h 40.9 m INFO 10:00:18,339 ProgressMeter - chr17:38490798 2.505219093E9 3.1 h 4.0 s 82.0% 3.8 h 40.7 m INFO 10:00:48,342 ProgressMeter - chr17:41119222 2.505219093E9 3.1 h 4.0 s 82.1% 3.8 h 40.6 m INFO 10:01:18,343 ProgressMeter - chr17:45007854 2.505219093E9 3.1 h 4.0 s 82.2% 3.8 h 40.4 m INFO 10:01:48,351 ProgressMeter - chr17:47684697 2.505219093E9 3.1 h 4.0 s 82.3% 3.8 h 40.2 m INFO 10:02:18,353 ProgressMeter - chr17:54806447 2.505219093E9 3.1 h 4.0 s 82.6% 3.8 h 39.7 m INFO 10:02:48,353 ProgressMeter - chr17:58921756 2.505219093E9 3.1 h 4.0 s 82.7% 3.8 h 39.5 m INFO 10:03:18,355 ProgressMeter - chr17:64297744 2.505219093E9 3.2 h 4.0 s 82.9% 3.8 h 39.1 m WARN 10:03:46,975 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr17:67634280 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 10:03:48,356 ProgressMeter - chr17:68034107 2.505219093E9 3.2 h 4.0 s 83.0% 3.8 h 38.9 m INFO 10:04:18,357 ProgressMeter - chr17:73391508 2.505219093E9 3.2 h 4.0 s 83.2% 3.8 h 38.5 m INFO 10:04:48,359 ProgressMeter - chr17:76884859 2.505219093E9 3.2 h 4.0 s 83.3% 3.8 h 38.3 m INFO 10:05:18,389 ProgressMeter - chr18:108585 2.586414303E9 3.2 h 4.0 s 83.4% 3.8 h 38.0 m INFO 10:05:48,391 ProgressMeter - chr18:6553320 2.586414303E9 3.2 h 4.0 s 83.6% 3.8 h 37.5 m INFO 10:06:18,393 ProgressMeter - chr18:11078042 2.586414303E9 3.2 h 4.0 s 83.8% 3.8 h 37.2 m INFO 10:06:48,425 ProgressMeter - chr18:20934106 2.586414303E9 3.2 h 4.0 s 84.1% 3.8 h 36.4 m INFO 10:07:18,427 ProgressMeter - chr18:33377366 2.586414303E9 3.2 h 4.0 s 84.5% 3.8 h 35.4 m INFO 10:07:48,429 ProgressMeter - chr18:45534500 2.586414303E9 3.2 h 4.0 s 84.9% 3.8 h 34.5 m INFO 10:08:18,430 ProgressMeter - chr18:53249571 2.586414303E9 3.2 h 4.0 s 85.1% 3.8 h 33.9 m INFO 10:08:48,431 ProgressMeter - chr18:57523796 2.586414303E9 3.2 h 4.0 s 85.3% 3.8 h 33.6 m INFO 10:09:18,432 ProgressMeter - chr18:65669655 2.586414303E9 3.3 h 4.0 s 85.5% 3.8 h 33.0 m INFO 10:09:48,433 ProgressMeter - chr18:75621107 2.586414303E9 3.3 h 4.0 s 85.9% 3.8 h 32.2 m INFO 10:10:18,436 ProgressMeter - chr19:1112467 2.664491551E9 3.3 h 4.0 s 86.0% 3.8 h 32.0 m INFO 10:10:48,437 ProgressMeter - chr19:4186758 2.664491551E9 3.3 h 4.0 s 86.1% 3.8 h 31.8 m INFO 10:11:18,445 ProgressMeter - chr19:6687661 2.664491551E9 3.3 h 4.0 s 86.1% 3.8 h 31.7 m INFO 10:11:48,446 ProgressMeter - chr19:7916263 2.664491551E9 3.3 h 4.0 s 86.2% 3.8 h 31.7 m INFO 10:12:18,448 ProgressMeter - chr19:10346682 2.664491551E9 3.3 h 4.0 s 86.3% 3.8 h 31.5 m INFO 10:12:48,449 ProgressMeter - chr19:11553705 2.664491551E9 3.3 h 4.0 s 86.3% 3.8 h 31.5 m INFO 10:13:18,450 ProgressMeter - chr19:14227445 2.664491551E9 3.3 h 4.0 s 86.4% 3.8 h 31.4 m INFO 10:13:48,467 ProgressMeter - chr19:17305874 2.664491551E9 3.3 h 4.0 s 86.5% 3.8 h 31.2 m INFO 10:14:18,468 ProgressMeter - chr19:19313022 2.664491551E9 3.3 h 4.0 s 86.6% 3.9 h 31.1 m INFO 10:14:48,478 ProgressMeter - chr19:30696132 2.664491551E9 3.3 h 4.0 s 86.9% 3.8 h 30.2 m INFO 10:15:18,480 ProgressMeter - chr19:36390467 2.664491551E9 3.4 h 4.0 s 87.1% 3.8 h 29.8 m INFO 10:15:48,481 ProgressMeter - chr19:39697164 2.664491551E9 3.4 h 4.0 s 87.2% 3.9 h 29.6 m INFO 10:16:18,482 ProgressMeter - chr19:42382730 2.664491551E9 3.4 h 4.0 s 87.3% 3.9 h 29.4 m INFO 10:16:48,483 ProgressMeter - chr19:45685482 2.664491551E9 3.4 h 4.0 s 87.4% 3.9 h 29.2 m INFO 10:17:18,511 ProgressMeter - chr19:47924503 2.664491551E9 3.4 h 4.0 s 87.5% 3.9 h 29.1 m WARN 10:17:20,719 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr19:47924167 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument WARN 10:17:20,860 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr19:47924197 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 10:17:48,584 ProgressMeter - chr19:49550431 2.664491551E9 3.4 h 4.0 s 87.5% 3.9 h 29.0 m INFO 10:18:18,586 ProgressMeter - chr19:52209391 2.664491551E9 3.4 h 4.0 s 87.6% 3.9 h 28.8 m INFO 10:18:48,589 ProgressMeter - chr19:54728611 2.664491551E9 3.4 h 4.0 s 87.7% 3.9 h 28.7 m INFO 10:19:18,590 ProgressMeter - chr19:55512685 2.664491551E9 3.4 h 4.0 s 87.7% 3.9 h 28.7 m INFO 10:19:48,591 ProgressMeter - chr19:58791618 2.664491551E9 3.4 h 4.0 s 87.8% 3.9 h 28.5 m INFO 10:20:18,598 ProgressMeter - chr20:3678888 2.723620534E9 3.4 h 4.0 s 88.0% 3.9 h 28.2 m INFO 10:20:48,600 ProgressMeter - chr20:12064432 2.723620534E9 3.4 h 4.0 s 88.2% 3.9 h 27.6 m INFO 10:21:18,601 ProgressMeter - chr20:22234547 2.723620534E9 3.5 h 4.0 s 88.6% 3.9 h 26.8 m INFO 10:21:48,602 ProgressMeter - chr20:31012599 2.723620534E9 3.5 h 4.0 s 88.8% 3.9 h 26.1 m INFO 10:22:18,639 ProgressMeter - chr20:36979374 2.723620534E9 3.5 h 4.0 s 89.0% 3.9 h 25.6 m INFO 10:22:48,641 ProgressMeter - chr20:42585442 2.723620534E9 3.5 h 4.0 s 89.2% 3.9 h 25.2 m INFO 10:23:18,643 ProgressMeter - chr20:44676054 2.723620534E9 3.5 h 4.0 s 89.3% 3.9 h 25.1 m INFO 10:23:48,644 ProgressMeter - chr20:47711013 2.723620534E9 3.5 h 4.0 s 89.4% 3.9 h 24.9 m INFO 10:24:18,645 ProgressMeter - chr20:50213596 2.723620534E9 3.5 h 4.0 s 89.5% 3.9 h 24.8 m INFO 10:24:48,728 ProgressMeter - chr20:58145354 2.723620534E9 3.5 h 4.0 s 89.7% 3.9 h 24.1 m INFO 10:25:18,730 ProgressMeter - chr21:2620901 2.786646054E9 3.5 h 4.0 s 90.0% 3.9 h 23.6 m INFO 10:25:48,731 ProgressMeter - chr21:16475977 2.786646054E9 3.5 h 4.0 s 90.4% 3.9 h 22.5 m INFO 10:26:18,742 ProgressMeter - chr21:27144010 2.786646054E9 3.5 h 4.0 s 90.7% 3.9 h 21.6 m INFO 10:26:48,882 ProgressMeter - chr21:33076006 2.786646054E9 3.5 h 4.0 s 90.9% 3.9 h 21.2 m INFO 10:27:19,125 ProgressMeter - chr21:34837624 2.786646054E9 3.6 h 4.0 s 91.0% 3.9 h 21.1 m INFO 10:27:49,129 ProgressMeter - chr21:36436088 2.786646054E9 3.6 h 4.0 s 91.0% 3.9 h 21.0 m WARN 10:27:51,182 ExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at chr21:36435857 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 10:28:19,132 ProgressMeter - chr21:38254066 2.786646054E9 3.6 h 4.0 s 91.1% 3.9 h 20.9 m INFO 10:28:49,571 ProgressMeter - chr21:43062016 2.786646054E9 3.6 h 4.0 s 91.3% 3.9 h 20.5 m INFO 10:29:19,573 ProgressMeter - chr21:46332209 2.786646054E9 3.6 h 4.0 s 91.4% 3.9 h 20.3 m INFO 10:29:49,878 ProgressMeter - chr22:13423001 2.834775949E9 3.6 h 4.0 s 91.9% 3.9 h 19.1 m INFO 10:30:19,880 ProgressMeter - chr22:19448927 2.834775949E9 3.6 h 4.0 s 92.0% 3.9 h 18.7 m INFO 10:30:49,883 ProgressMeter - chr22:22012015 2.834775949E9 3.6 h 4.0 s 92.1% 3.9 h 18.5 m INFO 10:31:19,885 ProgressMeter - chr22:25162107 2.834775949E9 3.6 h 4.0 s 92.2% 3.9 h 18.3 m INFO 10:31:50,331 ProgressMeter - chr22:29958274 2.834775949E9 3.6 h 4.0 s 92.4% 3.9 h 17.9 m INFO 10:32:20,395 ProgressMeter - chr22:30702585 2.834775949E9 3.6 h 4.0 s 92.4% 3.9 h 17.9 m INFO 10:32:50,398 ProgressMeter - chr22:35545049 2.834775949E9 3.6 h 4.0 s 92.6% 3.9 h 17.5 m INFO 10:33:20,400 ProgressMeter - chr22:37824807 2.834775949E9 3.7 h 4.0 s 92.6% 3.9 h 17.4 m INFO 10:33:50,588 ProgressMeter - chr22:40226055 2.834775949E9 3.7 h 4.0 s 92.7% 3.9 h 17.2 m INFO 10:34:20,876 ProgressMeter - chr22:43164590 2.834775949E9 3.7 h 4.0 s 92.8% 4.0 h 17.0 m INFO 10:34:51,176 ProgressMeter - chr22:46725596 2.834775949E9 3.7 h 4.0 s 92.9% 4.0 h 16.8 m INFO 10:35:21,179 ProgressMeter - chrX:1110101 2.886080515E9 3.7 h 4.0 s 93.1% 4.0 h 16.4 m INFO 10:35:51,552 ProgressMeter - chrX:12921283 2.886080515E9 3.7 h 4.0 s 93.5% 4.0 h 15.4 m INFO 10:36:21,554 ProgressMeter - chrX:21360802 2.886080515E9 3.7 h 4.0 s 93.8% 3.9 h 14.8 m INFO 10:36:51,556 ProgressMeter - chrX:31638855 2.886080515E9 3.7 h 4.0 s 94.1% 3.9 h 14.0 m INFO 10:37:21,559 ProgressMeter - chrX:40596988 2.886080515E9 3.7 h 4.0 s 94.4% 3.9 h 13.3 m INFO 10:37:51,561 ProgressMeter - chrX:48567658 2.886080515E9 3.7 h 4.0 s 94.6% 3.9 h 12.7 m INFO 10:38:21,563 ProgressMeter - chrX:59247438 2.886080515E9 3.7 h 4.0 s 95.0% 3.9 h 11.8 m INFO 10:38:51,852 ProgressMeter - chrX:70350517 2.886080515E9 3.7 h 4.0 s 95.3% 3.9 h 11.0 m INFO 10:39:21,855 ProgressMeter - chrX:79767451 2.886080515E9 3.8 h 4.0 s 95.6% 3.9 h 10.2 m INFO 10:39:51,863 ProgressMeter - chrX:91340616 2.886080515E9 3.8 h 4.0 s 96.0% 3.9 h 9.3 m INFO 10:40:22,265 ProgressMeter - chrX:101468263 2.886080515E9 3.8 h 4.0 s 96.3% 3.9 h 8.6 m INFO 10:40:52,267 ProgressMeter - chrX:109925915 2.886080515E9 3.8 h 4.0 s 96.6% 3.9 h 7.9 m INFO 10:41:22,268 ProgressMeter - chrX:120483057 2.886080515E9 3.8 h 4.0 s 97.0% 3.9 h 7.1 m INFO 10:41:52,274 ProgressMeter - chrX:131013931 2.886080515E9 3.8 h 4.0 s 97.3% 3.9 h 6.3 m INFO 10:42:22,276 ProgressMeter - chrX:142320010 2.886080515E9 3.8 h 4.0 s 97.7% 3.9 h 5.4 m INFO 10:42:52,692 ProgressMeter - chrX:152789052 2.886080515E9 3.8 h 4.0 s 98.0% 3.9 h 4.7 m INFO 10:43:22,695 ProgressMeter - chrY:9471813 3.041351075E9 3.8 h 4.0 s 98.4% 3.9 h 3.7 m INFO 10:43:52,697 ProgressMeter - chrY:33536332 3.041351075E9 3.8 h 4.0 s 99.2% 3.9 h 115.0 s INFO 10:44:23,014 ProgressMeter - chrY:52896532 3.041351075E9 3.8 h 4.0 s 99.8% 3.8 h 28.0 s INFO 10:44:45,436 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: 125 at org.broadinstitute.gatk.utils.sam.AlignmentUtils.calcNumHighQualitySoftClips(AlignmentUtils.java:437) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceModel.calcGenotypeLikelihoodsOfRefVsAny(ReferenceConfidenceModel.java:291) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.isActive(HaplotypeCaller.java:839) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.addIsActiveResult(TraverseActiveRegions.java:618) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.access$800(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:378) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee): ##### ERROR ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem. ##### ERROR If not, please post the error message, with stack trace, to the GATK forum. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: 125 ##### ERROR ------------------------------------------------------------------------------------------