INFO 16:01:38,261 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:01:38,271 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 INFO 16:01:38,271 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 16:01:38,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 16:01:38,279 HelpFormatter - Program Args: -T UnifiedGenotyper -R /PUBLIC_DATA/GENERATED/GenomeRef/chr_chrom_1kg_human_h37.fasta -alleles true_master_7.recode.vcf -L true_master_7.recode.vcf -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -stand_call_conf 0.0 -glm BOTH -G none -rf BadCigar -I B00G6SY_7.bam -o sortie.7.vcf INFO 16:01:38,289 HelpFormatter - Executing as sletort@Lanascol on Linux 3.2.0-52-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_55-b14. INFO 16:01:38,290 HelpFormatter - Date/Time: 2014/08/19 16:01:38 INFO 16:01:38,290 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:01:38,291 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:01:38,509 GenomeAnalysisEngine - Strictness is SILENT INFO 16:01:38,718 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 16:01:38,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 16:01:38,839 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10 INFO 16:01:40,742 RMDTrackBuilder - Writing Tribble index to disk for file /WORKING_DIRECTORY/sletort/support_équipe/MultiSample/by_chrom/true_master_7.recode.vcf.idx INFO 16:02:05,951 IntervalUtils - Processing 313587 bp from intervals INFO 16:02:06,164 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 16:02:06,678 GenomeAnalysisEngine - Done preparing for traversal INFO 16:02:06,678 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 16:02:06,679 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 16:02:06,679 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime WARN 16:02:08,628 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:299558, only considering the first record WARN 16:02:08,628 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:299558, only considering the first record WARN 16:02:09,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:551537, only considering the first record WARN 16:02:09,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:551537, only considering the first record WARN 16:02:09,876 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:716829, only considering the first record WARN 16:02:09,876 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:716829, only considering the first record WARN 16:02:10,346 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:796949, only considering the first record WARN 16:02:10,347 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:796949, only considering the first record WARN 16:02:10,348 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:796950, only considering the first record WARN 16:02:10,348 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:796950, only considering the first record WARN 16:02:10,852 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:821891, only considering the first record WARN 16:02:10,852 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:821891, only considering the first record WARN 16:02:11,364 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:882829, only considering the first record WARN 16:02:11,364 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:882829, only considering the first record WARN 16:02:11,656 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:891184, only considering the first record WARN 16:02:11,657 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:891184, only considering the first record WARN 16:02:11,912 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:894351, only considering the first record WARN 16:02:11,913 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:894351, only considering the first record WARN 16:02:12,337 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:916839, only considering the first record WARN 16:02:12,337 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:916839, only considering the first record WARN 16:02:12,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:916839, only considering the first record WARN 16:02:12,753 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:932074, only considering the first record WARN 16:02:12,753 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:932074, only considering the first record WARN 16:02:12,771 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:932270, only considering the first record WARN 16:02:12,771 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:932270, only considering the first record WARN 16:02:12,771 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:932270, only considering the first record WARN 16:02:13,460 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:940298, only considering the first record WARN 16:02:13,460 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:940298, only considering the first record WARN 16:02:13,680 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:944683, only considering the first record WARN 16:02:13,681 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:944683, only considering the first record WARN 16:02:13,697 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:944847, only considering the first record WARN 16:02:13,697 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:944847, only considering the first record WARN 16:02:13,738 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:944949, only considering the first record WARN 16:02:13,738 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:944949, only considering the first record WARN 16:02:13,799 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:945055, only considering the first record WARN 16:02:13,800 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:945055, only considering the first record WARN 16:02:13,836 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:945203, only considering the first record WARN 16:02:13,836 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:945203, only considering the first record WARN 16:02:13,836 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:945203, only considering the first record WARN 16:02:14,040 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:995450, only considering the first record WARN 16:02:14,040 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:995450, only considering the first record WARN 16:02:14,041 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:995464, only considering the first record WARN 16:02:14,041 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:995464, only considering the first record WARN 16:02:14,044 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:995476, only considering the first record WARN 16:02:14,045 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:995476, only considering the first record WARN 16:02:14,204 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1024002, only considering the first record WARN 16:02:14,205 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1024002, only considering the first record WARN 16:02:14,344 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1027672, only considering the first record WARN 16:02:14,345 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1027672, only considering the first record WARN 16:02:14,552 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1049589, only considering the first record WARN 16:02:14,553 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1049589, only considering the first record WARN 16:02:15,109 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1133514, only considering the first record WARN 16:02:15,109 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1133514, only considering the first record WARN 16:02:15,640 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1476678, only considering the first record WARN 16:02:15,641 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1476678, only considering the first record WARN 16:02:16,014 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1479055, only considering the first record WARN 16:02:16,015 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1479055, only considering the first record WARN 16:02:16,025 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1479055, only considering the first record WARN 16:02:16,084 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1479371, only considering the first record WARN 16:02:16,085 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1479371, only considering the first record WARN 16:02:16,909 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1509994, only considering the first record WARN 16:02:16,910 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1509994, only considering the first record WARN 16:02:17,049 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1511284, only considering the first record WARN 16:02:17,050 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1511284, only considering the first record WARN 16:02:18,434 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1528946, only considering the first record WARN 16:02:18,434 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1528946, only considering the first record WARN 16:02:18,435 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1528947, only considering the first record WARN 16:02:18,435 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1528947, only considering the first record WARN 16:02:18,715 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1533555, only considering the first record WARN 16:02:18,716 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1533555, only considering the first record WARN 16:02:19,001 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1537691, only considering the first record WARN 16:02:19,002 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1537691, only considering the first record WARN 16:02:19,002 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1537691, only considering the first record WARN 16:02:19,257 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1542123, only considering the first record WARN 16:02:19,257 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1542123, only considering the first record WARN 16:02:19,257 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1542125, only considering the first record WARN 16:02:19,258 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1542125, only considering the first record WARN 16:02:19,258 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1542125, only considering the first record WARN 16:02:19,451 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1545377, only considering the first record WARN 16:02:19,451 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1545377, only considering the first record WARN 16:02:19,511 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1546839, only considering the first record WARN 16:02:19,511 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1546839, only considering the first record WARN 16:02:19,511 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1546839, only considering the first record WARN 16:02:19,548 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1574721, only considering the first record WARN 16:02:19,548 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1574721, only considering the first record WARN 16:02:19,933 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1588959, only considering the first record WARN 16:02:19,933 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1588959, only considering the first record WARN 16:02:20,345 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1658400, only considering the first record WARN 16:02:20,345 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1658400, only considering the first record WARN 16:02:20,382 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1703343, only considering the first record WARN 16:02:20,383 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1703343, only considering the first record WARN 16:02:20,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1786949, only considering the first record WARN 16:02:20,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:1786949, only considering the first record WARN 16:02:20,982 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2020004, only considering the first record WARN 16:02:20,982 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2020004, only considering the first record WARN 16:02:21,700 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2280631, only considering the first record WARN 16:02:21,701 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2280631, only considering the first record WARN 16:02:22,900 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2416365, only considering the first record WARN 16:02:22,901 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2416365, only considering the first record WARN 16:02:22,901 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2416365, only considering the first record WARN 16:02:23,334 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2471776, only considering the first record WARN 16:02:23,335 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2471776, only considering the first record WARN 16:02:23,707 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2515179, only considering the first record WARN 16:02:23,707 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2515179, only considering the first record WARN 16:02:24,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2565578, only considering the first record WARN 16:02:24,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2565578, only considering the first record WARN 16:02:24,235 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2566230, only considering the first record WARN 16:02:24,236 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2566230, only considering the first record WARN 16:02:24,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2566966, only considering the first record WARN 16:02:24,266 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2566966, only considering the first record WARN 16:02:24,417 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2578237, only considering the first record WARN 16:02:24,417 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2578237, only considering the first record WARN 16:02:24,770 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2582153, only considering the first record WARN 16:02:24,771 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2582153, only considering the first record WARN 16:02:25,143 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2583831, only considering the first record WARN 16:02:25,144 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2583831, only considering the first record WARN 16:02:25,146 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2583834, only considering the first record WARN 16:02:25,146 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2583834, only considering the first record WARN 16:02:25,208 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2585130, only considering the first record WARN 16:02:25,208 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2585130, only considering the first record WARN 16:02:25,330 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2604727, only considering the first record WARN 16:02:25,330 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2604727, only considering the first record WARN 16:02:25,379 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2604767, only considering the first record WARN 16:02:25,379 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2604767, only considering the first record WARN 16:02:25,444 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2604890, only considering the first record WARN 16:02:25,444 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2604890, only considering the first record WARN 16:02:25,783 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2612351, only considering the first record WARN 16:02:25,783 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2612351, only considering the first record WARN 16:02:25,842 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2613598, only considering the first record WARN 16:02:25,843 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2613598, only considering the first record WARN 16:02:25,843 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2613598, only considering the first record WARN 16:02:26,226 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2619363, only considering the first record WARN 16:02:26,227 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2619363, only considering the first record WARN 16:02:26,937 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2641059, only considering the first record WARN 16:02:26,937 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2641059, only considering the first record WARN 16:02:27,114 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2647313, only considering the first record WARN 16:02:27,115 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2647313, only considering the first record WARN 16:02:27,683 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2700712, only considering the first record WARN 16:02:27,683 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2700712, only considering the first record WARN 16:02:27,844 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2741882, only considering the first record WARN 16:02:27,844 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2741882, only considering the first record WARN 16:02:27,905 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2748171, only considering the first record WARN 16:02:27,905 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2748171, only considering the first record WARN 16:02:28,036 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2749169, only considering the first record WARN 16:02:28,037 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2749169, only considering the first record WARN 16:02:28,037 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2749169, only considering the first record WARN 16:02:28,108 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2751688, only considering the first record WARN 16:02:28,109 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2751688, only considering the first record WARN 16:02:28,109 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2751688, only considering the first record WARN 16:02:28,109 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2751689, only considering the first record WARN 16:02:28,109 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2751689, only considering the first record WARN 16:02:28,110 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2751689, only considering the first record WARN 16:02:28,322 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2773035, only considering the first record WARN 16:02:28,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2773035, only considering the first record WARN 16:02:28,407 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2835261, only considering the first record WARN 16:02:28,407 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2835261, only considering the first record WARN 16:02:28,407 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2835261, only considering the first record WARN 16:02:28,466 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2949272, only considering the first record WARN 16:02:28,466 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2949272, only considering the first record WARN 16:02:29,242 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2971977, only considering the first record WARN 16:02:29,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2971977, only considering the first record WARN 16:02:29,458 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2983408, only considering the first record WARN 16:02:29,459 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2983408, only considering the first record WARN 16:02:29,459 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2983408, only considering the first record WARN 16:02:29,460 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2983418, only considering the first record WARN 16:02:29,460 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2983418, only considering the first record WARN 16:02:29,460 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:2983418, only considering the first record WARN 16:02:29,657 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3198256, only considering the first record WARN 16:02:29,657 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3198256, only considering the first record WARN 16:02:29,657 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3198256, only considering the first record WARN 16:02:29,658 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3198269, only considering the first record WARN 16:02:29,658 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3198269, only considering the first record WARN 16:02:29,658 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3198269, only considering the first record WARN 16:02:29,717 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3678092, only considering the first record WARN 16:02:29,718 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3678092, only considering the first record WARN 16:02:29,718 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3678092, only considering the first record WARN 16:02:29,720 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3678429, only considering the first record WARN 16:02:29,721 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3678429, only considering the first record WARN 16:02:29,721 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:3678429, only considering the first record WARN 16:02:30,025 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4013815, only considering the first record WARN 16:02:30,026 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4013815, only considering the first record WARN 16:02:30,026 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4013815, only considering the first record WARN 16:02:30,203 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4116191, only considering the first record WARN 16:02:30,203 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4116191, only considering the first record WARN 16:02:30,203 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4116191, only considering the first record WARN 16:02:30,473 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4171853, only considering the first record WARN 16:02:30,474 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4171853, only considering the first record WARN 16:02:30,612 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4201988, only considering the first record WARN 16:02:30,612 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4201988, only considering the first record WARN 16:02:30,882 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4259951, only considering the first record WARN 16:02:30,883 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4259951, only considering the first record WARN 16:02:30,885 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4260147, only considering the first record WARN 16:02:30,886 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4260147, only considering the first record WARN 16:02:30,886 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4260147, only considering the first record WARN 16:02:31,186 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4307963, only considering the first record WARN 16:02:31,186 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4307963, only considering the first record WARN 16:02:31,759 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4777070, only considering the first record WARN 16:02:31,760 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4777070, only considering the first record WARN 16:02:32,540 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4799660, only considering the first record WARN 16:02:32,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4799660, only considering the first record WARN 16:02:32,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4799660, only considering the first record WARN 16:02:32,865 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4820843, only considering the first record WARN 16:02:32,865 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4820843, only considering the first record WARN 16:02:33,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4824495, only considering the first record WARN 16:02:33,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4824495, only considering the first record WARN 16:02:34,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4845040, only considering the first record WARN 16:02:34,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4845040, only considering the first record WARN 16:02:34,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4845040, only considering the first record WARN 16:02:34,872 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4871879, only considering the first record WARN 16:02:34,872 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4871879, only considering the first record WARN 16:02:35,169 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4949063, only considering the first record WARN 16:02:35,169 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4949063, only considering the first record WARN 16:02:35,170 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4949063, only considering the first record WARN 16:02:35,207 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4951229, only considering the first record WARN 16:02:35,208 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4951229, only considering the first record WARN 16:02:35,208 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4951229, only considering the first record WARN 16:02:35,214 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4955381, only considering the first record WARN 16:02:35,214 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4955381, only considering the first record WARN 16:02:35,287 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4964954, only considering the first record WARN 16:02:35,288 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:4964954, only considering the first record WARN 16:02:35,337 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5021223, only considering the first record WARN 16:02:35,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5021223, only considering the first record WARN 16:02:35,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5021223, only considering the first record WARN 16:02:35,951 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5112554, only considering the first record WARN 16:02:35,952 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5112554, only considering the first record WARN 16:02:35,957 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5112809, only considering the first record WARN 16:02:35,957 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5112809, only considering the first record WARN 16:02:36,053 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5172046, only considering the first record WARN 16:02:36,053 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5172046, only considering the first record WARN 16:02:36,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5331002, only considering the first record INFO 16:02:36,689 ProgressMeter - chr7:5330925 2682745.0 30.0 s 11.0 s 7.3% 6.8 m 6.3 m WARN 16:02:36,711 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5331002, only considering the first record WARN 16:02:37,106 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5334881, only considering the first record WARN 16:02:37,107 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5334881, only considering the first record WARN 16:02:37,107 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5334881, only considering the first record WARN 16:02:37,742 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5354194, only considering the first record WARN 16:02:37,743 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5354194, only considering the first record WARN 16:02:37,757 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5354194, only considering the first record WARN 16:02:37,788 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5355905, only considering the first record WARN 16:02:37,788 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5355905, only considering the first record WARN 16:02:37,952 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5396461, only considering the first record WARN 16:02:37,953 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5396461, only considering the first record WARN 16:02:37,999 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5399458, only considering the first record WARN 16:02:37,999 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5399458, only considering the first record WARN 16:02:38,340 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5429577, only considering the first record WARN 16:02:38,340 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5429577, only considering the first record WARN 16:02:38,348 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5429989, only considering the first record WARN 16:02:38,348 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5429989, only considering the first record WARN 16:02:38,679 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5487160, only considering the first record WARN 16:02:38,680 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5487160, only considering the first record WARN 16:02:38,709 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5487456, only considering the first record WARN 16:02:38,709 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5487456, only considering the first record WARN 16:02:38,749 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5521036, only considering the first record WARN 16:02:38,749 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5521036, only considering the first record WARN 16:02:38,749 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5521036, only considering the first record WARN 16:02:38,843 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5539725, only considering the first record WARN 16:02:38,843 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5539725, only considering the first record WARN 16:02:39,260 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5568099, only considering the first record WARN 16:02:39,261 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5568099, only considering the first record WARN 16:02:39,926 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5662713, only considering the first record WARN 16:02:39,926 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5662713, only considering the first record WARN 16:02:40,239 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5770521, only considering the first record WARN 16:02:40,239 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5770521, only considering the first record WARN 16:02:40,287 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5779633, only considering the first record WARN 16:02:40,287 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5779633, only considering the first record WARN 16:02:40,299 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5780537, only considering the first record WARN 16:02:40,299 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5780537, only considering the first record WARN 16:02:40,550 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5920406, only considering the first record WARN 16:02:40,551 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5920406, only considering the first record WARN 16:02:40,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5921751, only considering the first record WARN 16:02:40,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5921751, only considering the first record WARN 16:02:40,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5921751, only considering the first record WARN 16:02:41,198 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5958792, only considering the first record WARN 16:02:41,199 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5958792, only considering the first record WARN 16:02:41,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5959840, only considering the first record WARN 16:02:41,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5959840, only considering the first record WARN 16:02:41,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5959840, only considering the first record WARN 16:02:41,281 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5965101, only considering the first record WARN 16:02:41,282 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5965101, only considering the first record WARN 16:02:41,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5966676, only considering the first record WARN 16:02:41,322 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5966676, only considering the first record WARN 16:02:41,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5982557, only considering the first record WARN 16:02:41,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5982557, only considering the first record WARN 16:02:41,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:5982557, only considering the first record WARN 16:02:41,630 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6005455, only considering the first record WARN 16:02:41,631 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6005455, only considering the first record WARN 16:02:41,738 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6017299, only considering the first record WARN 16:02:41,739 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6017299, only considering the first record WARN 16:02:41,782 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6018255, only considering the first record WARN 16:02:41,782 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6018255, only considering the first record WARN 16:02:42,299 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6027156, only considering the first record WARN 16:02:42,300 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6027156, only considering the first record WARN 16:02:42,712 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6035211, only considering the first record WARN 16:02:42,713 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6035211, only considering the first record WARN 16:02:43,164 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6057777, only considering the first record WARN 16:02:43,165 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6057777, only considering the first record WARN 16:02:43,329 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6064007, only considering the first record WARN 16:02:43,329 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6064007, only considering the first record WARN 16:02:43,527 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6066058, only considering the first record WARN 16:02:43,527 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6066058, only considering the first record WARN 16:02:44,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6080853, only considering the first record WARN 16:02:44,172 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6080853, only considering the first record WARN 16:02:44,397 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6088877, only considering the first record WARN 16:02:44,398 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6088877, only considering the first record WARN 16:02:44,499 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6097229, only considering the first record WARN 16:02:44,500 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6097229, only considering the first record WARN 16:02:44,651 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6175652, only considering the first record WARN 16:02:44,651 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6175652, only considering the first record WARN 16:02:44,927 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6185968, only considering the first record WARN 16:02:44,928 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6185968, only considering the first record WARN 16:02:45,098 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6192933, only considering the first record WARN 16:02:45,099 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6192933, only considering the first record WARN 16:02:45,614 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6230059, only considering the first record WARN 16:02:45,615 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6230059, only considering the first record WARN 16:02:45,750 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6414762, only considering the first record WARN 16:02:45,751 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6414762, only considering the first record WARN 16:02:46,000 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6441710, only considering the first record WARN 16:02:46,001 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6441710, only considering the first record WARN 16:02:46,042 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6449101, only considering the first record WARN 16:02:46,042 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6449101, only considering the first record WARN 16:02:46,042 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6449101, only considering the first record WARN 16:02:46,446 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6450511, only considering the first record WARN 16:02:46,601 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6450511, only considering the first record WARN 16:02:46,601 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6450511, only considering the first record WARN 16:02:46,761 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6460951, only considering the first record WARN 16:02:46,761 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6460951, only considering the first record WARN 16:02:47,030 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6469915, only considering the first record WARN 16:02:47,031 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6469915, only considering the first record WARN 16:02:47,282 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6475732, only considering the first record WARN 16:02:47,283 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6475732, only considering the first record WARN 16:02:47,283 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6475732, only considering the first record WARN 16:02:47,425 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6485942, only considering the first record WARN 16:02:47,426 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6485942, only considering the first record WARN 16:02:47,426 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6485942, only considering the first record WARN 16:02:48,570 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6544229, only considering the first record WARN 16:02:48,570 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6544229, only considering the first record WARN 16:02:49,660 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6620779, only considering the first record WARN 16:02:49,660 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6620779, only considering the first record WARN 16:02:49,661 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6620780, only considering the first record WARN 16:02:49,661 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6620780, only considering the first record WARN 16:02:49,837 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6622808, only considering the first record WARN 16:02:49,838 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6622808, only considering the first record WARN 16:02:49,987 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6625280, only considering the first record WARN 16:02:49,987 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6625280, only considering the first record WARN 16:02:50,157 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6633632, only considering the first record WARN 16:02:50,157 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6633632, only considering the first record WARN 16:02:50,157 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6633632, only considering the first record WARN 16:02:51,164 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6716546, only considering the first record WARN 16:02:51,164 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6716546, only considering the first record WARN 16:02:51,164 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6716546, only considering the first record WARN 16:02:51,250 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6732517, only considering the first record WARN 16:02:51,251 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6732517, only considering the first record WARN 16:02:51,340 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6737909, only considering the first record WARN 16:02:51,340 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6737909, only considering the first record WARN 16:02:51,354 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6745358, only considering the first record WARN 16:02:51,354 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6745358, only considering the first record WARN 16:02:51,354 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6745358, only considering the first record WARN 16:02:51,517 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6776799, only considering the first record WARN 16:02:51,590 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6776799, only considering the first record WARN 16:02:51,751 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6798600, only considering the first record WARN 16:02:51,751 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6798600, only considering the first record WARN 16:02:53,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6864614, only considering the first record WARN 16:02:53,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6864614, only considering the first record WARN 16:02:53,765 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:6864614, only considering the first record WARN 16:02:54,633 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7135440, only considering the first record WARN 16:02:54,633 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7135440, only considering the first record WARN 16:02:54,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7136061, only considering the first record WARN 16:02:54,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7136061, only considering the first record WARN 16:02:55,600 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7398640, only considering the first record WARN 16:02:55,601 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7398640, only considering the first record WARN 16:02:55,601 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7398640, only considering the first record WARN 16:02:55,787 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7413669, only considering the first record WARN 16:02:55,788 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7413669, only considering the first record WARN 16:02:55,788 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7413669, only considering the first record WARN 16:02:56,468 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7477619, only considering the first record WARN 16:02:56,469 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7477619, only considering the first record WARN 16:02:56,755 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7491860, only considering the first record WARN 16:02:56,756 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7491860, only considering the first record WARN 16:02:56,756 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7491873, only considering the first record WARN 16:02:56,756 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7491873, only considering the first record WARN 16:02:57,501 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7551281, only considering the first record WARN 16:02:57,501 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7551281, only considering the first record WARN 16:02:58,406 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7634493, only considering the first record WARN 16:02:58,407 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7634493, only considering the first record WARN 16:02:58,909 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7840967, only considering the first record WARN 16:02:58,910 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7840967, only considering the first record WARN 16:02:58,910 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:7840967, only considering the first record WARN 16:02:59,774 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:8196567, only considering the first record WARN 16:02:59,774 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:8196567, only considering the first record WARN 16:03:00,694 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11078824, only considering the first record WARN 16:03:00,695 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11078824, only considering the first record WARN 16:03:00,695 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11078824, only considering the first record WARN 16:03:00,741 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11101394, only considering the first record WARN 16:03:00,741 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11101394, only considering the first record WARN 16:03:00,773 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11151535, only considering the first record WARN 16:03:00,774 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11151535, only considering the first record WARN 16:03:00,774 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11151535, only considering the first record WARN 16:03:00,936 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11446788, only considering the first record WARN 16:03:00,936 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11446788, only considering the first record WARN 16:03:01,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11485146, only considering the first record WARN 16:03:01,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11485146, only considering the first record WARN 16:03:01,215 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11581570, only considering the first record WARN 16:03:01,216 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:11581570, only considering the first record WARN 16:03:01,395 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12258665, only considering the first record WARN 16:03:01,395 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12258665, only considering the first record WARN 16:03:01,396 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12258665, only considering the first record WARN 16:03:01,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12263798, only considering the first record WARN 16:03:01,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12263798, only considering the first record WARN 16:03:01,439 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12269260, only considering the first record WARN 16:03:01,440 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12269260, only considering the first record WARN 16:03:01,468 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12270565, only considering the first record WARN 16:03:01,469 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12270565, only considering the first record WARN 16:03:01,469 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12270565, only considering the first record WARN 16:03:01,550 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12375667, only considering the first record WARN 16:03:01,550 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12375667, only considering the first record WARN 16:03:01,636 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12381261, only considering the first record WARN 16:03:01,637 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12381261, only considering the first record WARN 16:03:01,637 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12381261, only considering the first record WARN 16:03:01,639 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12381370, only considering the first record WARN 16:03:01,639 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12381370, only considering the first record WARN 16:03:01,639 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12381370, only considering the first record WARN 16:03:01,795 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12394348, only considering the first record WARN 16:03:01,795 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12394348, only considering the first record WARN 16:03:01,891 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12400458, only considering the first record WARN 16:03:01,892 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12400458, only considering the first record WARN 16:03:01,892 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12400458, only considering the first record WARN 16:03:02,351 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12443823, only considering the first record WARN 16:03:02,351 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12443823, only considering the first record WARN 16:03:02,438 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12644347, only considering the first record WARN 16:03:02,439 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12644347, only considering the first record WARN 16:03:02,439 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12644348, only considering the first record WARN 16:03:02,439 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12644348, only considering the first record WARN 16:03:02,537 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12644499, only considering the first record WARN 16:03:02,538 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12644499, only considering the first record WARN 16:03:02,584 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12665056, only considering the first record WARN 16:03:02,585 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12665056, only considering the first record WARN 16:03:02,585 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12665056, only considering the first record WARN 16:03:02,606 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12666716, only considering the first record WARN 16:03:02,606 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12666716, only considering the first record WARN 16:03:02,606 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12666716, only considering the first record WARN 16:03:02,610 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12668342, only considering the first record WARN 16:03:02,610 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12668342, only considering the first record WARN 16:03:02,610 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12668342, only considering the first record WARN 16:03:02,683 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12683813, only considering the first record WARN 16:03:02,684 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:12683813, only considering the first record WARN 16:03:02,886 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:13979224, only considering the first record WARN 16:03:02,887 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:13979224, only considering the first record WARN 16:03:02,893 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14017126, only considering the first record WARN 16:03:02,893 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14017126, only considering the first record WARN 16:03:02,939 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14027867, only considering the first record WARN 16:03:02,940 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14027867, only considering the first record WARN 16:03:03,147 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14188873, only considering the first record WARN 16:03:03,148 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14188873, only considering the first record WARN 16:03:03,175 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14216345, only considering the first record WARN 16:03:03,176 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14216345, only considering the first record WARN 16:03:03,225 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14218035, only considering the first record WARN 16:03:03,225 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14218035, only considering the first record WARN 16:03:03,229 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14248798, only considering the first record WARN 16:03:03,229 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14248798, only considering the first record WARN 16:03:03,229 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14248798, only considering the first record WARN 16:03:03,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14248813, only considering the first record WARN 16:03:03,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14248813, only considering the first record WARN 16:03:03,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14248813, only considering the first record WARN 16:03:03,336 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14646782, only considering the first record WARN 16:03:03,337 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14646782, only considering the first record WARN 16:03:03,434 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14713025, only considering the first record WARN 16:03:03,434 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14713025, only considering the first record WARN 16:03:03,434 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14713025, only considering the first record WARN 16:03:03,454 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14724524, only considering the first record WARN 16:03:03,455 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14724524, only considering the first record WARN 16:03:03,476 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14737469, only considering the first record WARN 16:03:03,476 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14737469, only considering the first record WARN 16:03:03,491 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14737622, only considering the first record WARN 16:03:03,492 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14737622, only considering the first record WARN 16:03:03,642 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14794203, only considering the first record WARN 16:03:03,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14794203, only considering the first record WARN 16:03:03,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14794203, only considering the first record WARN 16:03:03,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14794213, only considering the first record WARN 16:03:03,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14794213, only considering the first record WARN 16:03:03,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14794213, only considering the first record WARN 16:03:03,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14797180, only considering the first record WARN 16:03:03,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14797180, only considering the first record WARN 16:03:03,666 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14880369, only considering the first record WARN 16:03:03,666 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14880369, only considering the first record WARN 16:03:03,675 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14881079, only considering the first record WARN 16:03:03,675 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:14881079, only considering the first record WARN 16:03:04,018 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15470269, only considering the first record WARN 16:03:04,018 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15470269, only considering the first record WARN 16:03:04,019 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15470269, only considering the first record WARN 16:03:04,021 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15470543, only considering the first record WARN 16:03:04,021 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15470543, only considering the first record WARN 16:03:04,032 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15584279, only considering the first record WARN 16:03:04,032 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15584279, only considering the first record WARN 16:03:04,169 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15666748, only considering the first record WARN 16:03:04,169 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15666748, only considering the first record WARN 16:03:04,170 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15666751, only considering the first record WARN 16:03:04,170 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:15666751, only considering the first record WARN 16:03:04,403 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16128995, only considering the first record WARN 16:03:04,403 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16128995, only considering the first record WARN 16:03:04,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16505054, only considering the first record WARN 16:03:04,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16505054, only considering the first record WARN 16:03:04,866 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16567080, only considering the first record WARN 16:03:04,866 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16567080, only considering the first record WARN 16:03:04,866 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16567080, only considering the first record WARN 16:03:05,407 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16713586, only considering the first record WARN 16:03:05,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16713586, only considering the first record WARN 16:03:05,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16713586, only considering the first record WARN 16:03:05,472 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16725501, only considering the first record WARN 16:03:05,472 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16725501, only considering the first record WARN 16:03:05,960 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16840641, only considering the first record WARN 16:03:05,960 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16840641, only considering the first record WARN 16:03:06,102 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16899723, only considering the first record WARN 16:03:06,102 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16899723, only considering the first record WARN 16:03:06,102 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16899723, only considering the first record WARN 16:03:06,158 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16901541, only considering the first record WARN 16:03:06,158 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:16901541, only considering the first record INFO 16:03:06,714 ProgressMeter - chr7:17383107 4221415.0 60.0 s 14.0 s 14.2% 7.0 m 6.0 m WARN 16:03:06,894 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17854575, only considering the first record WARN 16:03:06,895 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17854575, only considering the first record WARN 16:03:06,909 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17860809, only considering the first record WARN 16:03:06,909 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17860809, only considering the first record WARN 16:03:06,909 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17860809, only considering the first record WARN 16:03:07,136 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17884776, only considering the first record WARN 16:03:07,136 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17884776, only considering the first record WARN 16:03:07,727 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17913083, only considering the first record WARN 16:03:07,727 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17913083, only considering the first record WARN 16:03:07,830 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17930338, only considering the first record WARN 16:03:07,831 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17930338, only considering the first record WARN 16:03:07,831 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17930338, only considering the first record WARN 16:03:07,900 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17962382, only considering the first record WARN 16:03:07,901 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:17962382, only considering the first record WARN 16:03:08,397 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18067938, only considering the first record WARN 16:03:08,397 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18067938, only considering the first record WARN 16:03:08,398 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18067938, only considering the first record WARN 16:03:08,427 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18299946, only considering the first record WARN 16:03:08,427 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18299946, only considering the first record WARN 16:03:08,428 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18299946, only considering the first record WARN 16:03:08,779 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18535680, only considering the first record WARN 16:03:08,779 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18535680, only considering the first record WARN 16:03:08,805 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18624555, only considering the first record WARN 16:03:08,805 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18624555, only considering the first record WARN 16:03:08,805 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18624555, only considering the first record WARN 16:03:08,903 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18630481, only considering the first record WARN 16:03:08,903 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18630481, only considering the first record WARN 16:03:08,940 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18631098, only considering the first record WARN 16:03:08,940 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18631098, only considering the first record WARN 16:03:09,220 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18688033, only considering the first record WARN 16:03:09,220 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18688033, only considering the first record WARN 16:03:09,873 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18913624, only considering the first record WARN 16:03:09,873 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18913624, only considering the first record WARN 16:03:09,874 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:18913624, only considering the first record WARN 16:03:10,137 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:19156636, only considering the first record WARN 16:03:10,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:19156636, only considering the first record WARN 16:03:10,175 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:19184746, only considering the first record WARN 16:03:10,175 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:19184746, only considering the first record WARN 16:03:11,041 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20180463, only considering the first record WARN 16:03:11,041 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20180463, only considering the first record WARN 16:03:11,052 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20180507, only considering the first record WARN 16:03:11,052 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20180507, only considering the first record WARN 16:03:11,486 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20197411, only considering the first record WARN 16:03:11,487 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20197411, only considering the first record WARN 16:03:11,487 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20197411, only considering the first record WARN 16:03:12,519 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20444952, only considering the first record WARN 16:03:12,519 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20444952, only considering the first record WARN 16:03:12,520 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20444952, only considering the first record WARN 16:03:12,720 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20668768, only considering the first record WARN 16:03:12,721 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20668768, only considering the first record WARN 16:03:13,059 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20690192, only considering the first record WARN 16:03:13,059 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20690192, only considering the first record WARN 16:03:13,059 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20690192, only considering the first record WARN 16:03:13,317 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20720657, only considering the first record WARN 16:03:13,318 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20720657, only considering the first record WARN 16:03:13,318 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20720657, only considering the first record WARN 16:03:13,320 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20720738, only considering the first record WARN 16:03:13,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20720738, only considering the first record WARN 16:03:13,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20720738, only considering the first record WARN 16:03:13,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20737555, only considering the first record WARN 16:03:13,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20737555, only considering the first record WARN 16:03:13,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20737555, only considering the first record WARN 16:03:13,561 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738921, only considering the first record WARN 16:03:13,561 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738921, only considering the first record WARN 16:03:13,561 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738921, only considering the first record WARN 16:03:13,561 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738922, only considering the first record WARN 16:03:13,562 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738922, only considering the first record WARN 16:03:13,562 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738922, only considering the first record WARN 16:03:13,562 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738923, only considering the first record WARN 16:03:13,562 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738923, only considering the first record WARN 16:03:13,562 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20738923, only considering the first record WARN 16:03:13,565 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20739336, only considering the first record WARN 16:03:13,565 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20739336, only considering the first record WARN 16:03:13,575 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20739774, only considering the first record WARN 16:03:13,576 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20739774, only considering the first record WARN 16:03:13,770 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20802423, only considering the first record WARN 16:03:13,770 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20802423, only considering the first record WARN 16:03:13,797 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20803107, only considering the first record WARN 16:03:13,798 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:20803107, only considering the first record WARN 16:03:14,592 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21603750, only considering the first record WARN 16:03:14,593 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21603750, only considering the first record WARN 16:03:14,797 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21611562, only considering the first record WARN 16:03:14,798 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21611562, only considering the first record WARN 16:03:15,619 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21659549, only considering the first record WARN 16:03:15,619 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21659549, only considering the first record WARN 16:03:15,636 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21659554, only considering the first record WARN 16:03:15,636 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21659554, only considering the first record WARN 16:03:17,066 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21757807, only considering the first record WARN 16:03:17,066 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21757807, only considering the first record WARN 16:03:17,158 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21778172, only considering the first record WARN 16:03:17,159 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21778172, only considering the first record WARN 16:03:17,694 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21804843, only considering the first record WARN 16:03:17,694 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21804843, only considering the first record WARN 16:03:17,708 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21805227, only considering the first record WARN 16:03:17,709 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21805227, only considering the first record WARN 16:03:17,903 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21825920, only considering the first record WARN 16:03:17,903 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21825920, only considering the first record WARN 16:03:17,903 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21825920, only considering the first record WARN 16:03:18,018 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21828838, only considering the first record WARN 16:03:18,019 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21828838, only considering the first record WARN 16:03:18,077 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21829381, only considering the first record WARN 16:03:18,077 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21829381, only considering the first record WARN 16:03:18,078 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21829381, only considering the first record WARN 16:03:18,163 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21857458, only considering the first record WARN 16:03:18,163 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21857458, only considering the first record WARN 16:03:18,163 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21857458, only considering the first record WARN 16:03:19,443 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21905938, only considering the first record WARN 16:03:19,444 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21905938, only considering the first record WARN 16:03:19,511 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21907458, only considering the first record WARN 16:03:19,512 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21907458, only considering the first record WARN 16:03:19,540 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21907722, only considering the first record WARN 16:03:19,541 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21907722, only considering the first record WARN 16:03:19,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21913402, only considering the first record WARN 16:03:19,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21913402, only considering the first record WARN 16:03:19,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21913402, only considering the first record WARN 16:03:19,968 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21940815, only considering the first record WARN 16:03:19,969 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21940815, only considering the first record WARN 16:03:20,698 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21943524, only considering the first record WARN 16:03:20,698 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21943524, only considering the first record WARN 16:03:20,698 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21943524, only considering the first record WARN 16:03:21,080 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21951581, only considering the first record WARN 16:03:21,081 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:21951581, only considering the first record WARN 16:03:21,584 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22202772, only considering the first record WARN 16:03:21,585 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22202772, only considering the first record WARN 16:03:21,585 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22202772, only considering the first record WARN 16:03:21,778 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22270009, only considering the first record WARN 16:03:21,779 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22270009, only considering the first record WARN 16:03:22,137 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22357757, only considering the first record WARN 16:03:22,428 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22357757, only considering the first record WARN 16:03:23,006 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22478797, only considering the first record WARN 16:03:23,006 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22478797, only considering the first record WARN 16:03:23,006 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22478797, only considering the first record WARN 16:03:23,421 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22544571, only considering the first record WARN 16:03:23,421 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22544571, only considering the first record WARN 16:03:23,421 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22544571, only considering the first record WARN 16:03:23,543 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22766424, only considering the first record WARN 16:03:23,543 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22766424, only considering the first record WARN 16:03:23,543 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22766424, only considering the first record WARN 16:03:24,173 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22852643, only considering the first record WARN 16:03:24,174 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22852643, only considering the first record WARN 16:03:24,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22861549, only considering the first record WARN 16:03:24,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22861549, only considering the first record WARN 16:03:24,375 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22862612, only considering the first record WARN 16:03:24,375 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22862612, only considering the first record WARN 16:03:24,553 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22896681, only considering the first record WARN 16:03:24,553 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22896681, only considering the first record WARN 16:03:24,553 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22896681, only considering the first record WARN 16:03:24,556 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22984771, only considering the first record WARN 16:03:24,557 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22984771, only considering the first record WARN 16:03:24,557 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22984771, only considering the first record WARN 16:03:24,557 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22984772, only considering the first record WARN 16:03:24,557 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22984772, only considering the first record WARN 16:03:24,558 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:22984772, only considering the first record WARN 16:03:25,139 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23145137, only considering the first record WARN 16:03:25,139 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23145137, only considering the first record WARN 16:03:25,431 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23180197, only considering the first record WARN 16:03:25,431 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23180197, only considering the first record WARN 16:03:25,712 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23210526, only considering the first record WARN 16:03:25,713 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23210526, only considering the first record WARN 16:03:26,114 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23227218, only considering the first record WARN 16:03:26,114 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23227218, only considering the first record WARN 16:03:26,114 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23227218, only considering the first record WARN 16:03:26,126 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23227632, only considering the first record WARN 16:03:26,126 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23227632, only considering the first record WARN 16:03:26,927 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23339263, only considering the first record WARN 16:03:26,927 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23339263, only considering the first record WARN 16:03:27,261 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23347394, only considering the first record WARN 16:03:27,629 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23347394, only considering the first record WARN 16:03:28,601 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23529674, only considering the first record WARN 16:03:28,601 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23529674, only considering the first record WARN 16:03:28,629 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23531320, only considering the first record WARN 16:03:28,630 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23531320, only considering the first record WARN 16:03:28,658 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23545797, only considering the first record WARN 16:03:28,658 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23545797, only considering the first record WARN 16:03:28,670 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23546747, only considering the first record WARN 16:03:28,670 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23546747, only considering the first record WARN 16:03:28,709 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23552804, only considering the first record WARN 16:03:28,710 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23552804, only considering the first record WARN 16:03:28,825 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23624165, only considering the first record WARN 16:03:28,825 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23624165, only considering the first record WARN 16:03:28,825 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23624165, only considering the first record WARN 16:03:29,247 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23740853, only considering the first record WARN 16:03:29,247 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23740853, only considering the first record WARN 16:03:29,248 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23740853, only considering the first record WARN 16:03:30,155 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23776203, only considering the first record WARN 16:03:30,155 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23776203, only considering the first record WARN 16:03:30,269 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:23776203, only considering the first record WARN 16:03:30,883 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24331351, only considering the first record WARN 16:03:30,884 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24331351, only considering the first record WARN 16:03:30,917 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24664224, only considering the first record WARN 16:03:30,918 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24664224, only considering the first record WARN 16:03:30,918 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24664224, only considering the first record WARN 16:03:31,061 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24718285, only considering the first record WARN 16:03:31,061 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24718285, only considering the first record WARN 16:03:31,061 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24718285, only considering the first record WARN 16:03:31,082 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24719350, only considering the first record WARN 16:03:31,083 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24719350, only considering the first record WARN 16:03:31,083 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24719350, only considering the first record WARN 16:03:31,183 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24745614, only considering the first record WARN 16:03:31,183 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24745614, only considering the first record WARN 16:03:31,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24747318, only considering the first record WARN 16:03:31,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24747318, only considering the first record WARN 16:03:31,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24747318, only considering the first record WARN 16:03:31,698 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24783987, only considering the first record WARN 16:03:31,699 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24783987, only considering the first record WARN 16:03:31,807 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24840084, only considering the first record WARN 16:03:31,808 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24840084, only considering the first record WARN 16:03:31,838 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24846921, only considering the first record WARN 16:03:31,838 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24846921, only considering the first record WARN 16:03:31,838 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24846921, only considering the first record WARN 16:03:32,094 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24888404, only considering the first record WARN 16:03:32,094 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24888404, only considering the first record WARN 16:03:32,094 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24888404, only considering the first record WARN 16:03:32,135 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24901519, only considering the first record WARN 16:03:32,136 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24901519, only considering the first record WARN 16:03:32,316 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24912067, only considering the first record WARN 16:03:32,316 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24912067, only considering the first record WARN 16:03:32,316 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:24912067, only considering the first record WARN 16:03:32,483 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25176920, only considering the first record WARN 16:03:32,484 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25176920, only considering the first record WARN 16:03:32,485 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25176934, only considering the first record WARN 16:03:32,485 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25176934, only considering the first record WARN 16:03:32,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25198484, only considering the first record WARN 16:03:32,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25198484, only considering the first record WARN 16:03:32,617 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25198485, only considering the first record WARN 16:03:32,617 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25198485, only considering the first record WARN 16:03:32,619 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25200652, only considering the first record WARN 16:03:32,619 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:25200652, only considering the first record WARN 16:03:34,180 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26236868, only considering the first record WARN 16:03:34,212 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26236868, only considering the first record WARN 16:03:34,388 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26252202, only considering the first record WARN 16:03:34,389 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26252202, only considering the first record WARN 16:03:34,389 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26252202, only considering the first record WARN 16:03:34,480 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26396947, only considering the first record WARN 16:03:34,481 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26396947, only considering the first record WARN 16:03:35,125 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26724965, only considering the first record WARN 16:03:35,125 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26724965, only considering the first record WARN 16:03:35,126 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:26724965, only considering the first record WARN 16:03:36,130 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27141657, only considering the first record WARN 16:03:36,130 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27141657, only considering the first record WARN 16:03:36,500 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27168512, only considering the first record WARN 16:03:36,501 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27168512, only considering the first record INFO 16:03:36,716 ProgressMeter - chr7:27182747 5360566.0 90.0 s 16.0 s 19.7% 7.6 m 6.1 m WARN 16:03:36,798 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27185870, only considering the first record WARN 16:03:36,798 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27185870, only considering the first record WARN 16:03:36,799 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27185870, only considering the first record WARN 16:03:37,000 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27192088, only considering the first record WARN 16:03:37,001 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27192088, only considering the first record WARN 16:03:37,402 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27208712, only considering the first record WARN 16:03:37,402 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27208712, only considering the first record WARN 16:03:37,402 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27208712, only considering the first record WARN 16:03:37,729 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27224963, only considering the first record WARN 16:03:37,729 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27224963, only considering the first record WARN 16:03:37,730 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27224969, only considering the first record WARN 16:03:37,730 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27224969, only considering the first record WARN 16:03:38,045 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27282470, only considering the first record WARN 16:03:38,045 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27282470, only considering the first record WARN 16:03:38,142 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27283998, only considering the first record WARN 16:03:38,143 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27283998, only considering the first record WARN 16:03:38,366 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27566315, only considering the first record WARN 16:03:38,367 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27566315, only considering the first record WARN 16:03:38,367 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27566315, only considering the first record WARN 16:03:39,046 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27868483, only considering the first record WARN 16:03:39,047 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:27868483, only considering the first record WARN 16:03:40,473 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28535157, only considering the first record WARN 16:03:40,473 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28535157, only considering the first record WARN 16:03:40,473 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28535157, only considering the first record WARN 16:03:40,517 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28661876, only considering the first record WARN 16:03:40,518 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28661876, only considering the first record WARN 16:03:40,518 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28661876, only considering the first record WARN 16:03:40,764 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28726097, only considering the first record WARN 16:03:40,764 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:28726097, only considering the first record WARN 16:03:41,676 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29186800, only considering the first record WARN 16:03:41,676 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29186800, only considering the first record WARN 16:03:41,677 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29186800, only considering the first record WARN 16:03:41,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29332473, only considering the first record WARN 16:03:41,869 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29332473, only considering the first record WARN 16:03:41,877 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29393881, only considering the first record WARN 16:03:41,877 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29393881, only considering the first record WARN 16:03:41,883 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29394220, only considering the first record WARN 16:03:41,883 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29394220, only considering the first record WARN 16:03:41,959 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29437866, only considering the first record WARN 16:03:41,960 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29437866, only considering the first record WARN 16:03:42,054 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29535859, only considering the first record WARN 16:03:42,054 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29535859, only considering the first record WARN 16:03:42,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29544756, only considering the first record WARN 16:03:42,211 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29544756, only considering the first record WARN 16:03:42,211 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29544756, only considering the first record WARN 16:03:42,270 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29551906, only considering the first record WARN 16:03:42,271 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29551906, only considering the first record WARN 16:03:42,271 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29551907, only considering the first record WARN 16:03:42,271 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29551907, only considering the first record WARN 16:03:42,291 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29552796, only considering the first record WARN 16:03:42,291 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29552796, only considering the first record WARN 16:03:42,292 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29552796, only considering the first record WARN 16:03:42,409 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29720392, only considering the first record WARN 16:03:42,410 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29720392, only considering the first record WARN 16:03:42,785 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29966040, only considering the first record WARN 16:03:42,785 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29966040, only considering the first record WARN 16:03:42,817 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29979810, only considering the first record WARN 16:03:42,817 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29979810, only considering the first record WARN 16:03:42,817 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29979810, only considering the first record WARN 16:03:42,873 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29994979, only considering the first record WARN 16:03:42,873 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:29994979, only considering the first record WARN 16:03:42,936 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30030005, only considering the first record WARN 16:03:42,937 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30030005, only considering the first record WARN 16:03:42,952 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30055059, only considering the first record WARN 16:03:42,952 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30055059, only considering the first record WARN 16:03:42,953 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30055059, only considering the first record WARN 16:03:43,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30087380, only considering the first record WARN 16:03:43,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30087380, only considering the first record WARN 16:03:43,446 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30101683, only considering the first record WARN 16:03:43,446 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30101683, only considering the first record WARN 16:03:43,527 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30113617, only considering the first record WARN 16:03:43,527 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30113617, only considering the first record WARN 16:03:45,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30491527, only considering the first record WARN 16:03:46,101 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30491527, only considering the first record WARN 16:03:47,259 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30537153, only considering the first record WARN 16:03:47,501 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30537153, only considering the first record WARN 16:03:48,377 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30666596, only considering the first record WARN 16:03:48,377 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30666596, only considering the first record WARN 16:03:48,631 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30672330, only considering the first record WARN 16:03:48,631 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30672330, only considering the first record WARN 16:03:48,631 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30672330, only considering the first record WARN 16:03:49,157 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30793927, only considering the first record WARN 16:03:49,158 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30793927, only considering the first record WARN 16:03:49,322 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30805811, only considering the first record WARN 16:03:49,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30805811, only considering the first record WARN 16:03:49,889 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30821568, only considering the first record WARN 16:03:49,889 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30821568, only considering the first record WARN 16:03:49,911 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30821958, only considering the first record WARN 16:03:49,911 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30821958, only considering the first record WARN 16:03:50,733 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30962196, only considering the first record WARN 16:03:51,073 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:30962196, only considering the first record WARN 16:03:52,150 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31117023, only considering the first record WARN 16:03:52,151 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31117023, only considering the first record WARN 16:03:52,152 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31117096, only considering the first record WARN 16:03:52,152 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31117096, only considering the first record WARN 16:03:52,152 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31117096, only considering the first record WARN 16:03:52,276 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31125082, only considering the first record WARN 16:03:52,276 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31125082, only considering the first record WARN 16:03:53,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31697913, only considering the first record WARN 16:03:53,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31697913, only considering the first record WARN 16:03:53,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31735443, only considering the first record WARN 16:03:53,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31735443, only considering the first record WARN 16:03:53,309 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855260, only considering the first record WARN 16:03:53,309 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855260, only considering the first record WARN 16:03:53,332 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855754, only considering the first record WARN 16:03:53,332 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855754, only considering the first record WARN 16:03:53,335 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855967, only considering the first record WARN 16:03:53,335 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855967, only considering the first record WARN 16:03:53,335 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31855967, only considering the first record WARN 16:03:53,477 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31887438, only considering the first record WARN 16:03:53,478 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31887438, only considering the first record WARN 16:03:53,577 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31890707, only considering the first record WARN 16:03:53,578 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31890707, only considering the first record WARN 16:03:53,578 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31890715, only considering the first record WARN 16:03:53,579 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31890715, only considering the first record WARN 16:03:53,622 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31918134, only considering the first record WARN 16:03:53,622 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31918134, only considering the first record WARN 16:03:53,622 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:31918134, only considering the first record WARN 16:03:53,906 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32527660, only considering the first record WARN 16:03:53,906 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32527660, only considering the first record WARN 16:03:54,137 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32588821, only considering the first record WARN 16:03:54,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32588821, only considering the first record WARN 16:03:54,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32588821, only considering the first record WARN 16:03:54,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32588823, only considering the first record WARN 16:03:54,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32588823, only considering the first record WARN 16:03:54,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32588823, only considering the first record WARN 16:03:54,253 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32599205, only considering the first record WARN 16:03:54,254 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32599205, only considering the first record WARN 16:03:54,339 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32619219, only considering the first record WARN 16:03:54,339 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32619219, only considering the first record WARN 16:03:54,339 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:32619219, only considering the first record WARN 16:03:54,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33013811, only considering the first record WARN 16:03:54,777 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33013811, only considering the first record WARN 16:03:54,777 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33013811, only considering the first record WARN 16:03:55,028 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33054114, only considering the first record WARN 16:03:55,029 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33054114, only considering the first record WARN 16:03:55,029 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33054114, only considering the first record WARN 16:03:55,236 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33076070, only considering the first record WARN 16:03:55,237 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33076070, only considering the first record WARN 16:03:55,467 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33186329, only considering the first record WARN 16:03:55,467 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33186329, only considering the first record WARN 16:03:55,467 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33186329, only considering the first record WARN 16:03:55,517 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33195324, only considering the first record WARN 16:03:55,517 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33195324, only considering the first record WARN 16:03:56,024 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33946082, only considering the first record WARN 16:03:56,025 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33946082, only considering the first record WARN 16:03:56,025 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:33946082, only considering the first record WARN 16:03:56,134 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34014469, only considering the first record WARN 16:03:56,135 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34014469, only considering the first record WARN 16:03:56,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34097444, only considering the first record WARN 16:03:56,210 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34097444, only considering the first record WARN 16:03:56,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34687274, only considering the first record WARN 16:03:56,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34687274, only considering the first record WARN 16:03:56,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34687274, only considering the first record WARN 16:03:56,467 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34700152, only considering the first record WARN 16:03:56,467 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34700152, only considering the first record WARN 16:03:56,467 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34700152, only considering the first record WARN 16:03:56,496 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34725111, only considering the first record WARN 16:03:56,497 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34725111, only considering the first record WARN 16:03:56,521 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34725794, only considering the first record WARN 16:03:56,522 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34725794, only considering the first record WARN 16:03:56,522 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34725794, only considering the first record WARN 16:03:56,570 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34866499, only considering the first record WARN 16:03:56,570 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34866499, only considering the first record WARN 16:03:56,571 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34866499, only considering the first record WARN 16:03:56,588 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34867256, only considering the first record WARN 16:03:56,589 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34867256, only considering the first record WARN 16:03:56,876 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34979748, only considering the first record WARN 16:03:56,877 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34979748, only considering the first record WARN 16:03:57,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34997431, only considering the first record WARN 16:03:57,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34997431, only considering the first record WARN 16:03:57,144 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34997561, only considering the first record WARN 16:03:57,145 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:34997561, only considering the first record WARN 16:03:57,254 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35057134, only considering the first record WARN 16:03:57,254 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35057134, only considering the first record WARN 16:03:57,309 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35142432, only considering the first record WARN 16:03:57,310 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35142432, only considering the first record WARN 16:03:57,347 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35145941, only considering the first record WARN 16:03:57,348 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35145941, only considering the first record WARN 16:03:57,348 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35145941, only considering the first record WARN 16:03:57,468 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35284931, only considering the first record WARN 16:03:57,469 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35284931, only considering the first record WARN 16:03:57,469 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35284931, only considering the first record WARN 16:03:57,543 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35289889, only considering the first record WARN 16:03:57,544 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35289889, only considering the first record WARN 16:03:57,559 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35290247, only considering the first record WARN 16:03:57,559 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35290247, only considering the first record WARN 16:03:57,559 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35290247, only considering the first record WARN 16:03:57,706 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35840898, only considering the first record WARN 16:03:57,706 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35840898, only considering the first record WARN 16:03:57,737 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35851737, only considering the first record WARN 16:03:57,738 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35851737, only considering the first record WARN 16:03:57,738 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35851738, only considering the first record WARN 16:03:57,738 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35851738, only considering the first record WARN 16:03:57,759 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35871678, only considering the first record WARN 16:03:57,759 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35871678, only considering the first record WARN 16:03:57,905 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35919100, only considering the first record WARN 16:03:57,906 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35919100, only considering the first record WARN 16:03:57,906 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35919100, only considering the first record WARN 16:03:57,966 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35928097, only considering the first record WARN 16:03:57,967 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35928097, only considering the first record WARN 16:03:57,967 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35928097, only considering the first record WARN 16:03:57,971 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35928433, only considering the first record WARN 16:03:57,971 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:35928433, only considering the first record WARN 16:03:58,025 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36118292, only considering the first record WARN 16:03:58,026 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36118292, only considering the first record WARN 16:03:58,222 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36336303, only considering the first record WARN 16:03:58,223 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36336303, only considering the first record WARN 16:03:58,242 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36338412, only considering the first record WARN 16:03:58,242 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36338412, only considering the first record WARN 16:03:58,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36338413, only considering the first record WARN 16:03:58,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36338413, only considering the first record WARN 16:03:58,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36338413, only considering the first record WARN 16:03:58,407 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36407038, only considering the first record WARN 16:03:58,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36407038, only considering the first record WARN 16:03:58,809 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36455016, only considering the first record WARN 16:03:58,810 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36455016, only considering the first record WARN 16:03:58,810 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36455016, only considering the first record WARN 16:03:59,078 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36465193, only considering the first record WARN 16:03:59,078 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36465193, only considering the first record WARN 16:03:59,079 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36465194, only considering the first record WARN 16:03:59,079 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36465194, only considering the first record WARN 16:03:59,371 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36552790, only considering the first record WARN 16:03:59,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36552790, only considering the first record WARN 16:03:59,753 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36660968, only considering the first record WARN 16:03:59,753 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36660968, only considering the first record WARN 16:03:59,753 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:36660968, only considering the first record WARN 16:04:00,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37889482, only considering the first record WARN 16:04:00,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37889482, only considering the first record WARN 16:04:00,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37889482, only considering the first record WARN 16:04:00,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37889488, only considering the first record WARN 16:04:00,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37889488, only considering the first record WARN 16:04:00,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37889488, only considering the first record WARN 16:04:00,759 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37923589, only considering the first record WARN 16:04:00,759 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37923589, only considering the first record WARN 16:04:00,759 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37923589, only considering the first record WARN 16:04:01,392 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37990475, only considering the first record WARN 16:04:01,392 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:37990475, only considering the first record WARN 16:04:01,912 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38284924, only considering the first record WARN 16:04:01,913 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38284924, only considering the first record WARN 16:04:01,942 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38285118, only considering the first record WARN 16:04:01,942 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38285118, only considering the first record WARN 16:04:01,942 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38285118, only considering the first record WARN 16:04:02,046 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38301483, only considering the first record WARN 16:04:02,047 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38301483, only considering the first record WARN 16:04:02,047 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38301483, only considering the first record WARN 16:04:02,140 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38312847, only considering the first record WARN 16:04:02,141 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38312847, only considering the first record WARN 16:04:02,141 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38312847, only considering the first record WARN 16:04:02,157 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38315615, only considering the first record WARN 16:04:02,158 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38315615, only considering the first record WARN 16:04:02,958 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38431255, only considering the first record WARN 16:04:02,959 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38431255, only considering the first record WARN 16:04:02,971 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38431644, only considering the first record WARN 16:04:02,971 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38431644, only considering the first record WARN 16:04:03,124 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38462210, only considering the first record WARN 16:04:03,124 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38462210, only considering the first record WARN 16:04:03,133 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38466773, only considering the first record WARN 16:04:03,133 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38466773, only considering the first record WARN 16:04:03,137 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38467249, only considering the first record WARN 16:04:03,137 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38467249, only considering the first record WARN 16:04:03,137 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38467249, only considering the first record WARN 16:04:03,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38471148, only considering the first record WARN 16:04:03,230 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38471148, only considering the first record WARN 16:04:03,289 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38500872, only considering the first record WARN 16:04:03,290 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38500872, only considering the first record WARN 16:04:03,477 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38542650, only considering the first record WARN 16:04:03,478 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38542650, only considering the first record WARN 16:04:03,478 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38542650, only considering the first record WARN 16:04:03,536 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38543104, only considering the first record WARN 16:04:03,536 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38543104, only considering the first record WARN 16:04:04,033 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38798368, only considering the first record WARN 16:04:04,034 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38798368, only considering the first record WARN 16:04:04,034 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38798369, only considering the first record WARN 16:04:04,034 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38798369, only considering the first record WARN 16:04:04,054 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38805005, only considering the first record WARN 16:04:04,055 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38805005, only considering the first record WARN 16:04:04,055 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38805006, only considering the first record WARN 16:04:04,055 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38805006, only considering the first record WARN 16:04:04,198 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38829907, only considering the first record WARN 16:04:04,198 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38829907, only considering the first record WARN 16:04:04,198 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38829907, only considering the first record WARN 16:04:04,367 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857849, only considering the first record WARN 16:04:04,368 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857849, only considering the first record WARN 16:04:04,368 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857849, only considering the first record WARN 16:04:04,369 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857853, only considering the first record WARN 16:04:04,369 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857853, only considering the first record WARN 16:04:04,369 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857853, only considering the first record WARN 16:04:04,369 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857854, only considering the first record WARN 16:04:04,369 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857854, only considering the first record WARN 16:04:04,369 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38857854, only considering the first record WARN 16:04:04,376 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38860559, only considering the first record WARN 16:04:04,376 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38860559, only considering the first record WARN 16:04:04,387 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38861306, only considering the first record WARN 16:04:04,387 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38861306, only considering the first record WARN 16:04:04,387 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:38861306, only considering the first record WARN 16:04:04,661 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39378681, only considering the first record WARN 16:04:04,662 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39378681, only considering the first record WARN 16:04:04,662 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39378681, only considering the first record WARN 16:04:04,793 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39446015, only considering the first record WARN 16:04:04,794 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39446015, only considering the first record WARN 16:04:04,927 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39504670, only considering the first record WARN 16:04:04,927 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39504670, only considering the first record WARN 16:04:04,928 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39504670, only considering the first record WARN 16:04:05,158 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39725804, only considering the first record WARN 16:04:05,159 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39725804, only considering the first record WARN 16:04:05,159 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39725804, only considering the first record WARN 16:04:05,282 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39874544, only considering the first record WARN 16:04:05,283 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39874544, only considering the first record WARN 16:04:05,283 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:39874544, only considering the first record WARN 16:04:05,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40085185, only considering the first record WARN 16:04:05,409 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40085185, only considering the first record WARN 16:04:05,409 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40085185, only considering the first record WARN 16:04:05,484 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40118924, only considering the first record WARN 16:04:05,485 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40118924, only considering the first record WARN 16:04:05,485 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40118924, only considering the first record WARN 16:04:05,636 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40133522, only considering the first record WARN 16:04:05,636 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40133522, only considering the first record WARN 16:04:05,794 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40228034, only considering the first record WARN 16:04:05,795 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40228034, only considering the first record WARN 16:04:05,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40234821, only considering the first record WARN 16:04:05,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40234821, only considering the first record WARN 16:04:05,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40234825, only considering the first record WARN 16:04:05,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40234825, only considering the first record WARN 16:04:05,899 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40313672, only considering the first record WARN 16:04:05,899 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40313672, only considering the first record WARN 16:04:05,900 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40313672, only considering the first record WARN 16:04:05,943 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40488523, only considering the first record WARN 16:04:05,944 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40488523, only considering the first record WARN 16:04:05,946 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40488584, only considering the first record WARN 16:04:05,946 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:40488584, only considering the first record WARN 16:04:06,388 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:41740067, only considering the first record WARN 16:04:06,389 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:41740067, only considering the first record WARN 16:04:06,455 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42003663, only considering the first record WARN 16:04:06,455 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42003663, only considering the first record WARN 16:04:06,456 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42003663, only considering the first record INFO 16:04:06,718 ProgressMeter - chr7:42005656 6593682.0 120.0 s 18.0 s 27.5% 7.3 m 5.3 m WARN 16:04:07,330 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42012033, only considering the first record WARN 16:04:07,331 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42012033, only considering the first record WARN 16:04:07,514 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42116983, only considering the first record WARN 16:04:07,514 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42116983, only considering the first record WARN 16:04:07,519 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42187734, only considering the first record WARN 16:04:07,519 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42187734, only considering the first record WARN 16:04:07,586 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42262935, only considering the first record WARN 16:04:07,587 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42262935, only considering the first record WARN 16:04:07,595 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42948900, only considering the first record WARN 16:04:07,596 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42948900, only considering the first record WARN 16:04:07,739 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42957672, only considering the first record WARN 16:04:07,740 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42957672, only considering the first record WARN 16:04:07,740 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42957672, only considering the first record WARN 16:04:07,778 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42963978, only considering the first record WARN 16:04:07,779 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42963978, only considering the first record WARN 16:04:07,779 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42963978, only considering the first record WARN 16:04:07,830 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42964723, only considering the first record WARN 16:04:07,830 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42964723, only considering the first record WARN 16:04:07,862 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42966729, only considering the first record WARN 16:04:07,863 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42966729, only considering the first record WARN 16:04:07,863 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42966729, only considering the first record WARN 16:04:08,039 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42976286, only considering the first record WARN 16:04:08,040 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42976286, only considering the first record WARN 16:04:08,041 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:42976286, only considering the first record WARN 16:04:08,099 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43189976, only considering the first record WARN 16:04:08,100 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43189976, only considering the first record WARN 16:04:08,100 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43189976, only considering the first record WARN 16:04:08,722 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43548188, only considering the first record WARN 16:04:08,723 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43548188, only considering the first record WARN 16:04:08,723 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43548188, only considering the first record WARN 16:04:08,862 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43593987, only considering the first record WARN 16:04:08,862 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43593987, only considering the first record WARN 16:04:08,862 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43593987, only considering the first record WARN 16:04:08,963 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43684398, only considering the first record WARN 16:04:08,964 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43684398, only considering the first record WARN 16:04:09,181 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43847099, only considering the first record WARN 16:04:09,182 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43847099, only considering the first record WARN 16:04:09,182 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43847099, only considering the first record WARN 16:04:09,206 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43907119, only considering the first record WARN 16:04:09,206 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43907119, only considering the first record WARN 16:04:09,206 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43907119, only considering the first record WARN 16:04:09,513 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43921086, only considering the first record WARN 16:04:09,513 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:43921086, only considering the first record WARN 16:04:09,688 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44027049, only considering the first record WARN 16:04:09,688 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44027049, only considering the first record WARN 16:04:11,227 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44153115, only considering the first record WARN 16:04:11,228 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44153115, only considering the first record WARN 16:04:11,419 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44155243, only considering the first record WARN 16:04:11,426 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44155243, only considering the first record WARN 16:04:11,508 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44157770, only considering the first record WARN 16:04:11,509 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44157770, only considering the first record WARN 16:04:11,514 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44158087, only considering the first record WARN 16:04:11,514 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44158087, only considering the first record WARN 16:04:11,877 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44184848, only considering the first record WARN 16:04:11,877 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44184848, only considering the first record WARN 16:04:11,922 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44186077, only considering the first record WARN 16:04:11,922 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44186077, only considering the first record WARN 16:04:12,544 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44250280, only considering the first record WARN 16:04:12,545 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44250280, only considering the first record WARN 16:04:12,832 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44272314, only considering the first record WARN 16:04:12,832 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44272314, only considering the first record WARN 16:04:13,042 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44294324, only considering the first record WARN 16:04:13,043 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44294324, only considering the first record WARN 16:04:13,086 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44294367, only considering the first record WARN 16:04:13,086 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44294367, only considering the first record WARN 16:04:13,099 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44294372, only considering the first record WARN 16:04:13,099 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44294372, only considering the first record WARN 16:04:13,213 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44364010, only considering the first record WARN 16:04:13,213 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44364010, only considering the first record WARN 16:04:13,234 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44431835, only considering the first record WARN 16:04:13,234 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44431835, only considering the first record WARN 16:04:13,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44444379, only considering the first record WARN 16:04:13,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44444379, only considering the first record WARN 16:04:13,903 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44605732, only considering the first record WARN 16:04:13,904 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44605732, only considering the first record WARN 16:04:14,443 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44663890, only considering the first record WARN 16:04:14,443 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44663890, only considering the first record WARN 16:04:14,940 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44737717, only considering the first record WARN 16:04:14,940 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44737717, only considering the first record WARN 16:04:15,583 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44838941, only considering the first record WARN 16:04:15,583 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44838941, only considering the first record WARN 16:04:15,633 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44839996, only considering the first record WARN 16:04:15,633 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44839996, only considering the first record WARN 16:04:15,634 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44839997, only considering the first record WARN 16:04:15,634 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44839997, only considering the first record WARN 16:04:15,668 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44869202, only considering the first record WARN 16:04:15,669 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44869202, only considering the first record WARN 16:04:15,669 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:44869202, only considering the first record WARN 16:04:16,270 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45023343, only considering the first record WARN 16:04:16,271 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45023343, only considering the first record WARN 16:04:16,503 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45104769, only considering the first record WARN 16:04:16,503 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45104769, only considering the first record WARN 16:04:16,504 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45104769, only considering the first record WARN 16:04:17,320 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45143093, only considering the first record WARN 16:04:17,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45143093, only considering the first record WARN 16:04:18,555 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45957172, only considering the first record WARN 16:04:18,556 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:45957172, only considering the first record WARN 16:04:18,665 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:46736788, only considering the first record WARN 16:04:18,666 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:46736788, only considering the first record WARN 16:04:18,666 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:46736789, only considering the first record WARN 16:04:18,666 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:46736789, only considering the first record WARN 16:04:19,516 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47455308, only considering the first record WARN 16:04:19,516 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47455308, only considering the first record WARN 16:04:19,517 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47455308, only considering the first record WARN 16:04:19,611 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47474713, only considering the first record WARN 16:04:19,611 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47474713, only considering the first record WARN 16:04:19,611 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47474713, only considering the first record WARN 16:04:19,887 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47546547, only considering the first record WARN 16:04:19,887 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47546547, only considering the first record WARN 16:04:20,062 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47698746, only considering the first record WARN 16:04:20,062 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47698746, only considering the first record WARN 16:04:20,088 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47831911, only considering the first record WARN 16:04:20,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47831911, only considering the first record WARN 16:04:20,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47831911, only considering the first record WARN 16:04:20,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47831912, only considering the first record WARN 16:04:20,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47831912, only considering the first record WARN 16:04:20,089 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47831912, only considering the first record WARN 16:04:20,111 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47832645, only considering the first record WARN 16:04:20,112 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47832645, only considering the first record WARN 16:04:20,112 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47832645, only considering the first record WARN 16:04:20,429 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47860330, only considering the first record WARN 16:04:20,430 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47860330, only considering the first record WARN 16:04:20,975 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47916720, only considering the first record WARN 16:04:20,975 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47916720, only considering the first record WARN 16:04:20,975 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47916720, only considering the first record WARN 16:04:21,064 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47921785, only considering the first record WARN 16:04:21,064 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47921785, only considering the first record WARN 16:04:21,065 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47921788, only considering the first record WARN 16:04:21,065 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47921788, only considering the first record WARN 16:04:21,338 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47941630, only considering the first record WARN 16:04:21,339 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47941630, only considering the first record WARN 16:04:21,362 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47942418, only considering the first record WARN 16:04:21,362 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47942418, only considering the first record WARN 16:04:21,362 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47942418, only considering the first record WARN 16:04:21,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47982759, only considering the first record WARN 16:04:21,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47982759, only considering the first record WARN 16:04:21,617 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47982759, only considering the first record WARN 16:04:21,617 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47982760, only considering the first record WARN 16:04:21,617 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47982760, only considering the first record WARN 16:04:21,617 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:47982760, only considering the first record WARN 16:04:21,707 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48009017, only considering the first record WARN 16:04:21,707 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48009017, only considering the first record WARN 16:04:22,014 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48045523, only considering the first record WARN 16:04:22,014 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48045523, only considering the first record WARN 16:04:22,037 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48047105, only considering the first record WARN 16:04:22,037 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48047105, only considering the first record WARN 16:04:22,263 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48092847, only considering the first record WARN 16:04:22,263 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48092847, only considering the first record WARN 16:04:22,288 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48094446, only considering the first record WARN 16:04:22,289 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48094446, only considering the first record WARN 16:04:22,305 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48094483, only considering the first record WARN 16:04:22,305 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48094483, only considering the first record WARN 16:04:22,707 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48308447, only considering the first record WARN 16:04:22,707 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48308447, only considering the first record WARN 16:04:23,199 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48337383, only considering the first record WARN 16:04:23,200 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48337383, only considering the first record WARN 16:04:23,200 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48337383, only considering the first record WARN 16:04:23,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48450644, only considering the first record WARN 16:04:23,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48450644, only considering the first record WARN 16:04:23,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48450644, only considering the first record WARN 16:04:23,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48450647, only considering the first record WARN 16:04:23,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48450647, only considering the first record WARN 16:04:23,599 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48450647, only considering the first record WARN 16:04:23,768 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48522141, only considering the first record WARN 16:04:23,768 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48522141, only considering the first record WARN 16:04:23,768 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48522141, only considering the first record WARN 16:04:23,802 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48522844, only considering the first record WARN 16:04:23,802 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48522844, only considering the first record WARN 16:04:23,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48547760, only considering the first record WARN 16:04:23,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48547760, only considering the first record WARN 16:04:23,871 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48550502, only considering the first record WARN 16:04:23,872 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48550502, only considering the first record WARN 16:04:24,073 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48684730, only considering the first record WARN 16:04:24,074 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48684730, only considering the first record WARN 16:04:24,074 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:48684730, only considering the first record WARN 16:04:24,381 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:49951519, only considering the first record WARN 16:04:24,382 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:49951519, only considering the first record WARN 16:04:24,427 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50057879, only considering the first record WARN 16:04:24,427 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50057879, only considering the first record WARN 16:04:24,428 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50057919, only considering the first record WARN 16:04:24,428 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50057919, only considering the first record WARN 16:04:24,525 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50157027, only considering the first record WARN 16:04:24,525 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50157027, only considering the first record WARN 16:04:24,615 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50181406, only considering the first record WARN 16:04:24,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50181406, only considering the first record WARN 16:04:24,616 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50181406, only considering the first record WARN 16:04:25,004 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50537677, only considering the first record WARN 16:04:25,005 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50537677, only considering the first record WARN 16:04:25,092 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50545910, only considering the first record WARN 16:04:25,092 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50545910, only considering the first record WARN 16:04:25,094 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50547181, only considering the first record WARN 16:04:25,094 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50547181, only considering the first record WARN 16:04:25,117 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50547726, only considering the first record WARN 16:04:25,117 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50547726, only considering the first record WARN 16:04:25,190 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50595563, only considering the first record WARN 16:04:25,191 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50595563, only considering the first record WARN 16:04:25,191 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50595563, only considering the first record WARN 16:04:25,260 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50608193, only considering the first record WARN 16:04:25,261 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50608193, only considering the first record WARN 16:04:25,261 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50608193, only considering the first record WARN 16:04:25,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50661077, only considering the first record WARN 16:04:25,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50661077, only considering the first record WARN 16:04:25,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50661077, only considering the first record WARN 16:04:25,360 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50663299, only considering the first record WARN 16:04:25,360 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:50663299, only considering the first record WARN 16:04:26,133 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:51098569, only considering the first record WARN 16:04:26,133 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:51098569, only considering the first record WARN 16:04:27,381 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54636365, only considering the first record WARN 16:04:27,381 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54636365, only considering the first record WARN 16:04:27,381 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54636365, only considering the first record WARN 16:04:27,414 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54824665, only considering the first record WARN 16:04:27,414 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54824665, only considering the first record WARN 16:04:27,414 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54824665, only considering the first record WARN 16:04:27,415 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54824915, only considering the first record WARN 16:04:27,415 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54824915, only considering the first record WARN 16:04:27,416 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:54824915, only considering the first record WARN 16:04:27,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55002841, only considering the first record WARN 16:04:27,598 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55002841, only considering the first record WARN 16:04:27,629 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55004044, only considering the first record WARN 16:04:27,629 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55004044, only considering the first record WARN 16:04:27,653 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55004800, only considering the first record WARN 16:04:27,653 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55004800, only considering the first record WARN 16:04:27,784 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55219092, only considering the first record WARN 16:04:27,784 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55219092, only considering the first record WARN 16:04:28,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234375, only considering the first record WARN 16:04:28,171 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234375, only considering the first record WARN 16:04:28,176 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234429, only considering the first record WARN 16:04:28,177 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234429, only considering the first record WARN 16:04:28,180 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234484, only considering the first record WARN 16:04:28,180 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234484, only considering the first record WARN 16:04:28,180 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55234484, only considering the first record WARN 16:04:28,203 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55236528, only considering the first record WARN 16:04:28,203 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55236528, only considering the first record WARN 16:04:28,204 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55236528, only considering the first record WARN 16:04:28,308 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55241678, only considering the first record WARN 16:04:28,309 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55241678, only considering the first record WARN 16:04:28,630 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242464, only considering the first record WARN 16:04:28,631 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242464, only considering the first record WARN 16:04:28,726 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242466, only considering the first record WARN 16:04:28,726 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242466, only considering the first record WARN 16:04:28,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242468, only considering the first record WARN 16:04:28,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242468, only considering the first record WARN 16:04:28,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242469, only considering the first record WARN 16:04:28,867 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242469, only considering the first record WARN 16:04:28,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242470, only considering the first record WARN 16:04:28,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55242470, only considering the first record WARN 16:04:29,194 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55249004, only considering the first record WARN 16:04:29,194 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55249004, only considering the first record WARN 16:04:29,195 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55249005, only considering the first record WARN 16:04:29,195 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55249005, only considering the first record WARN 16:04:29,195 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55249012, only considering the first record WARN 16:04:29,196 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55249012, only considering the first record WARN 16:04:29,740 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55460026, only considering the first record WARN 16:04:29,741 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55460026, only considering the first record WARN 16:04:29,822 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55469243, only considering the first record WARN 16:04:29,823 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55469243, only considering the first record WARN 16:04:29,823 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55469243, only considering the first record WARN 16:04:29,843 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55492812, only considering the first record WARN 16:04:29,843 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55492812, only considering the first record WARN 16:04:30,215 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55758681, only considering the first record WARN 16:04:30,215 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55758681, only considering the first record WARN 16:04:30,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55774631, only considering the first record WARN 16:04:30,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55774631, only considering the first record WARN 16:04:30,243 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55774631, only considering the first record WARN 16:04:30,361 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55832142, only considering the first record WARN 16:04:30,361 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55832142, only considering the first record WARN 16:04:30,392 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55832762, only considering the first record WARN 16:04:30,392 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55832762, only considering the first record WARN 16:04:30,524 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55910301, only considering the first record WARN 16:04:30,524 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55910301, only considering the first record WARN 16:04:30,525 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:55910301, only considering the first record WARN 16:04:30,847 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56059457, only considering the first record WARN 16:04:30,848 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56059457, only considering the first record WARN 16:04:30,848 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56059457, only considering the first record WARN 16:04:30,876 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56064851, only considering the first record WARN 16:04:30,877 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56064851, only considering the first record WARN 16:04:30,966 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56084856, only considering the first record WARN 16:04:30,966 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56084856, only considering the first record WARN 16:04:30,989 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56085117, only considering the first record WARN 16:04:30,990 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56085117, only considering the first record WARN 16:04:31,026 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56087605, only considering the first record WARN 16:04:31,026 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56087605, only considering the first record WARN 16:04:31,044 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56088563, only considering the first record WARN 16:04:31,044 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56088563, only considering the first record WARN 16:04:31,049 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56088726, only considering the first record WARN 16:04:31,049 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56088726, only considering the first record WARN 16:04:31,116 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56120494, only considering the first record WARN 16:04:31,117 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56120494, only considering the first record WARN 16:04:31,337 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56129361, only considering the first record WARN 16:04:31,337 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56129361, only considering the first record WARN 16:04:31,621 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56142876, only considering the first record WARN 16:04:31,621 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56142876, only considering the first record WARN 16:04:31,621 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56142876, only considering the first record WARN 16:04:31,652 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56145045, only considering the first record WARN 16:04:31,652 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56145045, only considering the first record WARN 16:04:31,797 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56147953, only considering the first record WARN 16:04:31,797 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56147953, only considering the first record WARN 16:04:31,797 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56147953, only considering the first record WARN 16:04:31,953 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56149477, only considering the first record WARN 16:04:31,954 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56149477, only considering the first record WARN 16:04:32,151 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56157149, only considering the first record WARN 16:04:32,152 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56157149, only considering the first record WARN 16:04:32,255 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56174389, only considering the first record WARN 16:04:32,255 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:56174389, only considering the first record WARN 16:04:32,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57069439, only considering the first record WARN 16:04:32,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57069439, only considering the first record WARN 16:04:32,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57069439, only considering the first record WARN 16:04:32,383 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57071827, only considering the first record WARN 16:04:32,384 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57071827, only considering the first record WARN 16:04:32,551 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57521865, only considering the first record WARN 16:04:32,552 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57521865, only considering the first record WARN 16:04:32,552 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:57521865, only considering the first record WARN 16:04:32,939 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:63033299, only considering the first record WARN 16:04:32,939 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:63033299, only considering the first record WARN 16:04:33,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:63673169, only considering the first record WARN 16:04:33,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:63673169, only considering the first record WARN 16:04:33,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:63673169, only considering the first record WARN 16:04:33,981 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64166536, only considering the first record WARN 16:04:33,982 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64166536, only considering the first record WARN 16:04:33,983 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64166642, only considering the first record WARN 16:04:33,983 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64166642, only considering the first record WARN 16:04:34,174 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64169019, only considering the first record WARN 16:04:34,174 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64169019, only considering the first record WARN 16:04:34,736 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64312496, only considering the first record WARN 16:04:34,737 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64312496, only considering the first record WARN 16:04:34,737 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64312496, only considering the first record WARN 16:04:34,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64377105, only considering the first record WARN 16:04:34,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64377105, only considering the first record WARN 16:04:34,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64377105, only considering the first record WARN 16:04:34,984 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64389507, only considering the first record WARN 16:04:34,985 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64389507, only considering the first record WARN 16:04:34,985 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64389507, only considering the first record WARN 16:04:34,985 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64389512, only considering the first record WARN 16:04:34,986 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64389512, only considering the first record WARN 16:04:34,986 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64389512, only considering the first record WARN 16:04:35,075 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64441359, only considering the first record WARN 16:04:35,076 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64441359, only considering the first record WARN 16:04:35,076 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64441359, only considering the first record WARN 16:04:35,452 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64639926, only considering the first record WARN 16:04:35,452 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:64639926, only considering the first record WARN 16:04:35,664 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65150824, only considering the first record WARN 16:04:35,664 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65150824, only considering the first record WARN 16:04:36,264 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65444359, only considering the first record WARN 16:04:36,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65444359, only considering the first record INFO 16:04:36,720 ProgressMeter - chr7:65553793 8644336.0 2.5 m 17.0 s 37.0% 6.8 m 4.3 m WARN 16:04:36,915 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65557448, only considering the first record WARN 16:04:36,915 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65557448, only considering the first record WARN 16:04:37,020 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65593101, only considering the first record WARN 16:04:37,020 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65593101, only considering the first record WARN 16:04:37,020 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65593101, only considering the first record WARN 16:04:37,072 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65599246, only considering the first record WARN 16:04:37,073 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65599246, only considering the first record WARN 16:04:37,078 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65599532, only considering the first record WARN 16:04:37,079 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65599532, only considering the first record WARN 16:04:37,079 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65599532, only considering the first record WARN 16:04:37,182 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751804, only considering the first record WARN 16:04:37,182 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751804, only considering the first record WARN 16:04:37,182 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751806, only considering the first record WARN 16:04:37,182 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751806, only considering the first record WARN 16:04:37,183 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751807, only considering the first record WARN 16:04:37,183 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751807, only considering the first record WARN 16:04:37,183 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751810, only considering the first record WARN 16:04:37,183 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65751810, only considering the first record WARN 16:04:37,322 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65842543, only considering the first record WARN 16:04:37,322 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65842543, only considering the first record WARN 16:04:37,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65842545, only considering the first record WARN 16:04:37,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:65842545, only considering the first record WARN 16:04:37,397 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66099100, only considering the first record WARN 16:04:37,398 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66099100, only considering the first record WARN 16:04:37,398 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66099100, only considering the first record WARN 16:04:37,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66099748, only considering the first record WARN 16:04:37,408 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66099748, only considering the first record WARN 16:04:37,507 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66135881, only considering the first record WARN 16:04:37,507 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66135881, only considering the first record WARN 16:04:37,507 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66135881, only considering the first record WARN 16:04:37,671 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66264668, only considering the first record WARN 16:04:37,672 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66264668, only considering the first record WARN 16:04:37,672 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66264668, only considering the first record WARN 16:04:37,673 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66269743, only considering the first record WARN 16:04:37,673 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66269743, only considering the first record WARN 16:04:37,674 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66269743, only considering the first record WARN 16:04:37,723 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66406381, only considering the first record WARN 16:04:37,723 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66406381, only considering the first record WARN 16:04:37,724 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66406381, only considering the first record WARN 16:04:37,990 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66456737, only considering the first record WARN 16:04:37,990 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66456737, only considering the first record WARN 16:04:38,130 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66459025, only considering the first record WARN 16:04:38,130 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66459025, only considering the first record WARN 16:04:38,351 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66489771, only considering the first record WARN 16:04:38,352 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66489771, only considering the first record WARN 16:04:38,360 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66514511, only considering the first record WARN 16:04:38,361 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66514511, only considering the first record WARN 16:04:38,361 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66514511, only considering the first record WARN 16:04:38,526 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66648684, only considering the first record WARN 16:04:38,526 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66648684, only considering the first record WARN 16:04:38,527 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66648684, only considering the first record WARN 16:04:38,545 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66703238, only considering the first record WARN 16:04:38,545 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:66703238, only considering the first record WARN 16:04:39,678 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70255577, only considering the first record WARN 16:04:39,679 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70255577, only considering the first record WARN 16:04:39,701 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70256076, only considering the first record WARN 16:04:39,701 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70256076, only considering the first record WARN 16:04:39,721 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70598391, only considering the first record WARN 16:04:39,722 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70598391, only considering the first record WARN 16:04:39,722 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:70598391, only considering the first record WARN 16:04:39,959 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:71253268, only considering the first record WARN 16:04:39,960 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:71253268, only considering the first record WARN 16:04:39,960 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:71253268, only considering the first record WARN 16:04:40,552 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72301117, only considering the first record WARN 16:04:40,552 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72301117, only considering the first record WARN 16:04:41,112 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72436915, only considering the first record WARN 16:04:41,112 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72436915, only considering the first record WARN 16:04:41,112 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72436915, only considering the first record WARN 16:04:41,669 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72754919, only considering the first record WARN 16:04:41,669 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:72754919, only considering the first record WARN 16:04:42,730 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73020725, only considering the first record WARN 16:04:42,730 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73020725, only considering the first record WARN 16:04:43,461 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73122620, only considering the first record WARN 16:04:43,461 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73122620, only considering the first record WARN 16:04:43,850 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73254462, only considering the first record WARN 16:04:43,851 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73254462, only considering the first record WARN 16:04:44,268 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73463398, only considering the first record WARN 16:04:44,269 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73463398, only considering the first record WARN 16:04:44,642 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73483531, only considering the first record WARN 16:04:44,642 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73483531, only considering the first record WARN 16:04:45,185 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73636048, only considering the first record WARN 16:04:45,186 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73636048, only considering the first record WARN 16:04:45,508 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73753628, only considering the first record WARN 16:04:45,509 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73753628, only considering the first record WARN 16:04:45,509 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73753628, only considering the first record WARN 16:04:45,810 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73816301, only considering the first record WARN 16:04:45,810 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73816301, only considering the first record WARN 16:04:45,850 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73923020, only considering the first record WARN 16:04:45,850 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73923020, only considering the first record WARN 16:04:45,861 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73926955, only considering the first record WARN 16:04:45,861 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73926955, only considering the first record WARN 16:04:46,090 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73961090, only considering the first record WARN 16:04:46,091 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:73961090, only considering the first record WARN 16:04:46,246 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:74105220, only considering the first record WARN 16:04:46,246 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:74105220, only considering the first record WARN 16:04:46,370 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:74131650, only considering the first record WARN 16:04:46,370 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:74131650, only considering the first record WARN 16:04:46,370 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:74131650, only considering the first record WARN 16:04:47,222 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75115178, only considering the first record WARN 16:04:47,223 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75115178, only considering the first record WARN 16:04:47,327 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75145267, only considering the first record WARN 16:04:47,328 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75145267, only considering the first record WARN 16:04:47,379 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75167891, only considering the first record WARN 16:04:47,379 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75167891, only considering the first record WARN 16:04:47,379 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75167891, only considering the first record WARN 16:04:47,438 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75173710, only considering the first record WARN 16:04:47,438 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75173710, only considering the first record WARN 16:04:47,440 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75173729, only considering the first record WARN 16:04:47,440 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75173729, only considering the first record WARN 16:04:47,576 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75184494, only considering the first record WARN 16:04:47,577 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75184494, only considering the first record WARN 16:04:47,577 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75184494, only considering the first record WARN 16:04:47,586 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75184866, only considering the first record WARN 16:04:47,586 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75184866, only considering the first record WARN 16:04:47,649 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75186655, only considering the first record WARN 16:04:47,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75186655, only considering the first record WARN 16:04:47,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75186655, only considering the first record WARN 16:04:47,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75186660, only considering the first record WARN 16:04:47,650 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75186660, only considering the first record WARN 16:04:47,651 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75186660, only considering the first record WARN 16:04:47,831 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75228522, only considering the first record WARN 16:04:47,831 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75228522, only considering the first record WARN 16:04:47,898 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75442247, only considering the first record WARN 16:04:47,899 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75442247, only considering the first record WARN 16:04:47,899 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75442247, only considering the first record WARN 16:04:47,922 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75508179, only considering the first record WARN 16:04:47,922 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75508179, only considering the first record WARN 16:04:47,945 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75510232, only considering the first record WARN 16:04:47,945 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75510232, only considering the first record WARN 16:04:49,113 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75635116, only considering the first record WARN 16:04:49,114 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75635116, only considering the first record WARN 16:04:49,165 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75651323, only considering the first record WARN 16:04:49,165 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75651323, only considering the first record WARN 16:04:49,188 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75659317, only considering the first record WARN 16:04:49,189 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75659317, only considering the first record WARN 16:04:49,278 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75692509, only considering the first record WARN 16:04:49,278 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:75692509, only considering the first record WARN 16:04:49,741 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76023088, only considering the first record WARN 16:04:49,741 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76023088, only considering the first record WARN 16:04:49,798 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76024085, only considering the first record WARN 16:04:49,799 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76024085, only considering the first record WARN 16:04:49,799 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76024085, only considering the first record WARN 16:04:50,050 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76059074, only considering the first record WARN 16:04:50,051 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76059074, only considering the first record WARN 16:04:51,051 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76256104, only considering the first record WARN 16:04:51,051 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76256104, only considering the first record WARN 16:04:51,121 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76632644, only considering the first record WARN 16:04:51,121 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76632644, only considering the first record WARN 16:04:51,350 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76751907, only considering the first record WARN 16:04:51,350 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76751907, only considering the first record WARN 16:04:51,350 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76751907, only considering the first record WARN 16:04:51,590 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76889256, only considering the first record WARN 16:04:51,591 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76889256, only considering the first record WARN 16:04:51,628 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76902823, only considering the first record WARN 16:04:51,629 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76902823, only considering the first record WARN 16:04:51,629 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76902823, only considering the first record WARN 16:04:51,694 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76904398, only considering the first record WARN 16:04:51,695 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76904398, only considering the first record WARN 16:04:51,695 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76904398, only considering the first record WARN 16:04:51,702 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76908050, only considering the first record WARN 16:04:51,702 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76908050, only considering the first record WARN 16:04:51,921 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76940131, only considering the first record WARN 16:04:51,922 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76940131, only considering the first record WARN 16:04:51,922 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76940131, only considering the first record WARN 16:04:52,040 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76942606, only considering the first record WARN 16:04:52,041 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76942606, only considering the first record WARN 16:04:52,043 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76942753, only considering the first record WARN 16:04:52,044 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76942753, only considering the first record WARN 16:04:52,195 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76958956, only considering the first record WARN 16:04:52,196 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76958956, only considering the first record WARN 16:04:52,199 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76959378, only considering the first record WARN 16:04:52,200 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76959378, only considering the first record WARN 16:04:52,200 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76959378, only considering the first record WARN 16:04:52,212 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76959908, only considering the first record WARN 16:04:52,213 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76959908, only considering the first record WARN 16:04:52,410 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76984752, only considering the first record WARN 16:04:52,410 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:76984752, only considering the first record WARN 16:04:53,645 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77538486, only considering the first record WARN 16:04:53,645 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77538486, only considering the first record WARN 16:04:53,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77583929, only considering the first record WARN 16:04:53,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77583929, only considering the first record WARN 16:04:53,778 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77583932, only considering the first record WARN 16:04:53,778 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77583932, only considering the first record WARN 16:04:53,829 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77708105, only considering the first record WARN 16:04:53,829 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77708105, only considering the first record WARN 16:04:53,831 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77708127, only considering the first record WARN 16:04:53,831 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77708127, only considering the first record WARN 16:04:53,832 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77708129, only considering the first record WARN 16:04:53,832 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77708129, only considering the first record WARN 16:04:54,020 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77765066, only considering the first record WARN 16:04:54,020 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77765066, only considering the first record WARN 16:04:54,021 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77765066, only considering the first record WARN 16:04:54,127 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77885127, only considering the first record WARN 16:04:54,127 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:77885127, only considering the first record WARN 16:04:54,189 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:78119221, only considering the first record WARN 16:04:54,190 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:78119221, only considering the first record WARN 16:04:54,195 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:78130801, only considering the first record WARN 16:04:54,195 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:78130801, only considering the first record WARN 16:04:54,331 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79764174, only considering the first record WARN 16:04:54,332 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79764174, only considering the first record WARN 16:04:54,332 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79764186, only considering the first record WARN 16:04:54,332 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79764186, only considering the first record WARN 16:04:54,374 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79833464, only considering the first record WARN 16:04:54,374 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79833464, only considering the first record WARN 16:04:54,374 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79833464, only considering the first record WARN 16:04:54,388 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79841648, only considering the first record WARN 16:04:54,389 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79841648, only considering the first record WARN 16:04:54,398 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79846514, only considering the first record WARN 16:04:54,398 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:79846514, only considering the first record WARN 16:04:54,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80285893, only considering the first record WARN 16:04:54,643 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80285893, only considering the first record WARN 16:04:54,711 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80293264, only considering the first record WARN 16:04:54,711 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80293264, only considering the first record WARN 16:04:54,711 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80293264, only considering the first record WARN 16:04:54,887 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80300474, only considering the first record WARN 16:04:54,888 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80300474, only considering the first record WARN 16:04:55,117 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80374789, only considering the first record WARN 16:04:55,117 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80374789, only considering the first record WARN 16:04:55,276 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80394898, only considering the first record WARN 16:04:55,276 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:80394898, only considering the first record WARN 16:04:55,734 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81358607, only considering the first record WARN 16:04:55,735 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81358607, only considering the first record WARN 16:04:55,735 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81358607, only considering the first record WARN 16:04:55,751 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81359116, only considering the first record WARN 16:04:55,751 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81359116, only considering the first record WARN 16:04:56,196 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81598298, only considering the first record WARN 16:04:56,196 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81598298, only considering the first record WARN 16:04:56,274 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81603871, only considering the first record WARN 16:04:56,275 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81603871, only considering the first record WARN 16:04:56,284 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81604102, only considering the first record WARN 16:04:56,284 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81604102, only considering the first record WARN 16:04:56,285 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81604102, only considering the first record WARN 16:04:56,290 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81604343, only considering the first record WARN 16:04:56,290 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81604343, only considering the first record WARN 16:04:56,290 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81604343, only considering the first record WARN 16:04:56,331 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81614512, only considering the first record WARN 16:04:56,331 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81614512, only considering the first record WARN 16:04:56,527 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81689481, only considering the first record WARN 16:04:56,528 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81689481, only considering the first record WARN 16:04:56,528 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81689481, only considering the first record WARN 16:04:56,529 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81689527, only considering the first record WARN 16:04:56,529 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81689527, only considering the first record WARN 16:04:56,529 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81689527, only considering the first record WARN 16:04:56,581 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81695857, only considering the first record WARN 16:04:56,581 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81695857, only considering the first record WARN 16:04:56,672 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81765862, only considering the first record WARN 16:04:56,672 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81765862, only considering the first record WARN 16:04:56,702 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81799648, only considering the first record WARN 16:04:56,702 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:81799648, only considering the first record WARN 16:04:56,820 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82390259, only considering the first record WARN 16:04:56,821 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82390259, only considering the first record WARN 16:04:56,821 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82390259, only considering the first record WARN 16:04:57,030 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82475316, only considering the first record WARN 16:04:57,030 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82475316, only considering the first record WARN 16:04:57,030 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82475316, only considering the first record WARN 16:04:58,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997521, only considering the first record WARN 16:04:58,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997521, only considering the first record WARN 16:04:58,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997521, only considering the first record WARN 16:04:58,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997523, only considering the first record WARN 16:04:58,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997523, only considering the first record WARN 16:04:58,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997523, only considering the first record WARN 16:04:58,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997524, only considering the first record WARN 16:04:58,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997524, only considering the first record WARN 16:04:58,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:82997524, only considering the first record WARN 16:04:58,633 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83022355, only considering the first record WARN 16:04:58,634 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83022355, only considering the first record WARN 16:04:58,634 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83022355, only considering the first record WARN 16:04:58,686 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83023898, only considering the first record WARN 16:04:58,687 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83023898, only considering the first record WARN 16:04:58,687 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83023898, only considering the first record WARN 16:04:58,772 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83035894, only considering the first record WARN 16:04:58,772 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83035894, only considering the first record WARN 16:04:58,772 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83035894, only considering the first record WARN 16:04:58,840 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83048206, only considering the first record WARN 16:04:58,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83048206, only considering the first record WARN 16:04:58,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83048206, only considering the first record WARN 16:04:58,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83048207, only considering the first record WARN 16:04:58,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83048207, only considering the first record WARN 16:04:58,841 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83048207, only considering the first record WARN 16:04:58,859 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83096373, only considering the first record WARN 16:04:58,860 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83096373, only considering the first record WARN 16:04:58,860 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83096373, only considering the first record WARN 16:04:58,863 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83098428, only considering the first record WARN 16:04:58,863 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83098428, only considering the first record WARN 16:04:58,870 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83098714, only considering the first record WARN 16:04:58,870 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83098714, only considering the first record WARN 16:04:58,941 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83278227, only considering the first record WARN 16:04:58,941 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83278227, only considering the first record WARN 16:04:58,944 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83590263, only considering the first record WARN 16:04:58,944 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83590263, only considering the first record WARN 16:04:58,944 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83590263, only considering the first record WARN 16:04:59,002 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83606595, only considering the first record WARN 16:04:59,002 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83606595, only considering the first record WARN 16:04:59,052 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83630994, only considering the first record WARN 16:04:59,052 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83630994, only considering the first record WARN 16:04:59,052 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83630994, only considering the first record WARN 16:04:59,130 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640052, only considering the first record WARN 16:04:59,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640052, only considering the first record WARN 16:04:59,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640052, only considering the first record WARN 16:04:59,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640059, only considering the first record WARN 16:04:59,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640059, only considering the first record WARN 16:04:59,131 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640059, only considering the first record WARN 16:04:59,132 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640062, only considering the first record WARN 16:04:59,132 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640062, only considering the first record WARN 16:04:59,132 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83640062, only considering the first record WARN 16:04:59,300 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83824112, only considering the first record WARN 16:04:59,300 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83824112, only considering the first record WARN 16:04:59,301 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83824340, only considering the first record WARN 16:04:59,301 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83824340, only considering the first record WARN 16:04:59,302 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83824368, only considering the first record WARN 16:04:59,303 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:83824368, only considering the first record WARN 16:04:59,568 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:84694722, only considering the first record WARN 16:04:59,569 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:84694722, only considering the first record WARN 16:04:59,765 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86493380, only considering the first record WARN 16:04:59,765 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86493380, only considering the first record WARN 16:04:59,975 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86547414, only considering the first record WARN 16:04:59,976 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86547414, only considering the first record WARN 16:04:59,976 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86547414, only considering the first record WARN 16:05:00,452 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86803666, only considering the first record WARN 16:05:00,453 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86803666, only considering the first record WARN 16:05:00,453 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86803666, only considering the first record WARN 16:05:00,486 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86804340, only considering the first record WARN 16:05:00,486 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86804340, only considering the first record WARN 16:05:00,486 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:86804340, only considering the first record WARN 16:05:01,362 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87027106, only considering the first record WARN 16:05:01,362 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87027106, only considering the first record WARN 16:05:01,363 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87027106, only considering the first record WARN 16:05:01,618 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87049119, only considering the first record WARN 16:05:01,618 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87049119, only considering the first record WARN 16:05:02,269 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87133480, only considering the first record WARN 16:05:02,270 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87133480, only considering the first record WARN 16:05:02,307 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87134124, only considering the first record WARN 16:05:02,308 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87134124, only considering the first record WARN 16:05:02,308 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87134124, only considering the first record WARN 16:05:02,456 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87149237, only considering the first record WARN 16:05:02,456 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87149237, only considering the first record WARN 16:05:02,457 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87149237, only considering the first record WARN 16:05:02,870 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87193475, only considering the first record WARN 16:05:02,871 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87193475, only considering the first record WARN 16:05:03,268 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87330326, only considering the first record WARN 16:05:03,268 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87330326, only considering the first record WARN 16:05:03,269 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87330326, only considering the first record WARN 16:05:03,329 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87459755, only considering the first record WARN 16:05:03,330 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87459755, only considering the first record WARN 16:05:03,330 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87459755, only considering the first record WARN 16:05:03,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87470474, only considering the first record WARN 16:05:03,372 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87470474, only considering the first record WARN 16:05:03,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87470474, only considering the first record WARN 16:05:03,607 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87526550, only considering the first record WARN 16:05:03,607 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87526550, only considering the first record WARN 16:05:03,835 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87704798, only considering the first record WARN 16:05:03,836 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87704798, only considering the first record WARN 16:05:03,836 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87704799, only considering the first record WARN 16:05:03,836 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87704799, only considering the first record WARN 16:05:03,954 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87757952, only considering the first record WARN 16:05:03,954 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87757952, only considering the first record WARN 16:05:04,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87772152, only considering the first record WARN 16:05:04,138 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87772152, only considering the first record WARN 16:05:04,354 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87807933, only considering the first record WARN 16:05:04,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87807933, only considering the first record WARN 16:05:04,355 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87807933, only considering the first record WARN 16:05:04,380 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87813172, only considering the first record WARN 16:05:04,380 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87813172, only considering the first record WARN 16:05:04,380 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87813172, only considering the first record WARN 16:05:04,540 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87843965, only considering the first record WARN 16:05:04,540 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87843965, only considering the first record WARN 16:05:04,540 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:87843965, only considering the first record WARN 16:05:04,971 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88424365, only considering the first record WARN 16:05:04,972 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88424365, only considering the first record WARN 16:05:05,068 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88957140, only considering the first record WARN 16:05:05,069 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88957140, only considering the first record WARN 16:05:05,069 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88957140, only considering the first record WARN 16:05:05,250 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88964225, only considering the first record WARN 16:05:05,251 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:88964225, only considering the first record WARN 16:05:05,521 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89778900, only considering the first record WARN 16:05:05,541 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89778900, only considering the first record WARN 16:05:05,627 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89791622, only considering the first record WARN 16:05:05,628 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89791622, only considering the first record WARN 16:05:05,980 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89859612, only considering the first record WARN 16:05:05,980 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89859612, only considering the first record WARN 16:05:06,123 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89894836, only considering the first record WARN 16:05:06,124 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89894836, only considering the first record WARN 16:05:06,181 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89908833, only considering the first record WARN 16:05:06,181 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89908833, only considering the first record WARN 16:05:06,231 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89916275, only considering the first record WARN 16:05:06,231 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89916275, only considering the first record WARN 16:05:06,277 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89929110, only considering the first record WARN 16:05:06,277 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89929110, only considering the first record WARN 16:05:06,280 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89929478, only considering the first record WARN 16:05:06,280 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89929478, only considering the first record WARN 16:05:06,280 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:89929478, only considering the first record INFO 16:05:06,723 ProgressMeter - chr7:90003465 1.076735E7 3.0 m 16.0 s 48.1% 6.2 m 3.2 m WARN 16:05:06,728 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90004133, only considering the first record WARN 16:05:06,729 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90004133, only considering the first record WARN 16:05:06,729 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90004133, only considering the first record WARN 16:05:06,895 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90419385, only considering the first record WARN 16:05:06,896 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90419385, only considering the first record WARN 16:05:06,896 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90419385, only considering the first record WARN 16:05:06,897 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90419416, only considering the first record WARN 16:05:06,897 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90419416, only considering the first record WARN 16:05:06,897 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90419416, only considering the first record WARN 16:05:06,951 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90493013, only considering the first record WARN 16:05:06,952 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90493013, only considering the first record WARN 16:05:06,952 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90493013, only considering the first record WARN 16:05:06,984 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90613401, only considering the first record WARN 16:05:06,985 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:90613401, only considering the first record WARN 16:05:07,314 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91609809, only considering the first record WARN 16:05:07,314 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91609809, only considering the first record WARN 16:05:07,314 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91609809, only considering the first record WARN 16:05:07,328 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91621992, only considering the first record WARN 16:05:07,328 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91621992, only considering the first record WARN 16:05:07,373 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91625067, only considering the first record WARN 16:05:07,374 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91625067, only considering the first record WARN 16:05:07,607 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91668019, only considering the first record WARN 16:05:07,608 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91668019, only considering the first record WARN 16:05:07,760 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91681599, only considering the first record WARN 16:05:07,761 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91681599, only considering the first record WARN 16:05:07,761 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91681599, only considering the first record WARN 16:05:07,924 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91706402, only considering the first record WARN 16:05:07,925 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91706402, only considering the first record WARN 16:05:07,926 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91706406, only considering the first record WARN 16:05:07,926 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91706406, only considering the first record WARN 16:05:07,928 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91706410, only considering the first record WARN 16:05:07,928 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91706410, only considering the first record WARN 16:05:08,003 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91711791, only considering the first record WARN 16:05:08,004 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91711791, only considering the first record WARN 16:05:08,153 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91725656, only considering the first record WARN 16:05:08,153 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91725656, only considering the first record WARN 16:05:08,153 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91725656, only considering the first record WARN 16:05:08,409 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91730750, only considering the first record WARN 16:05:08,409 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91730750, only considering the first record WARN 16:05:08,409 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91730750, only considering the first record WARN 16:05:08,412 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731477, only considering the first record WARN 16:05:08,412 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731477, only considering the first record WARN 16:05:08,412 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731477, only considering the first record WARN 16:05:08,413 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731481, only considering the first record WARN 16:05:08,413 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731481, only considering the first record WARN 16:05:08,413 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731481, only considering the first record WARN 16:05:08,413 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731484, only considering the first record WARN 16:05:08,413 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731484, only considering the first record WARN 16:05:08,413 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91731484, only considering the first record WARN 16:05:08,494 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91738363, only considering the first record WARN 16:05:08,495 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91738363, only considering the first record WARN 16:05:08,495 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:91738363, only considering the first record WARN 16:05:10,011 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92129161, only considering the first record WARN 16:05:10,011 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92129161, only considering the first record WARN 16:05:10,315 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92134726, only considering the first record WARN 16:05:10,315 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92134726, only considering the first record WARN 16:05:10,315 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92134726, only considering the first record WARN 16:05:10,321 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92135419, only considering the first record WARN 16:05:10,322 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92135419, only considering the first record WARN 16:05:10,474 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92136499, only considering the first record WARN 16:05:10,475 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92136499, only considering the first record WARN 16:05:10,483 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92138449, only considering the first record WARN 16:05:10,483 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92138449, only considering the first record WARN 16:05:10,918 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92166620, only considering the first record WARN 16:05:10,918 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92166620, only considering the first record WARN 16:05:11,684 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92764982, only considering the first record WARN 16:05:11,685 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92764982, only considering the first record WARN 16:05:11,754 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92826723, only considering the first record WARN 16:05:11,754 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92826723, only considering the first record WARN 16:05:11,776 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92827050, only considering the first record WARN 16:05:11,777 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92827050, only considering the first record WARN 16:05:11,868 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92845242, only considering the first record WARN 16:05:11,869 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92845242, only considering the first record WARN 16:05:11,949 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92869562, only considering the first record WARN 16:05:11,949 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92869562, only considering the first record WARN 16:05:11,949 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92869562, only considering the first record WARN 16:05:11,950 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92869564, only considering the first record WARN 16:05:11,950 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92869564, only considering the first record WARN 16:05:11,950 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92869564, only considering the first record WARN 16:05:11,975 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92885515, only considering the first record WARN 16:05:11,975 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92885515, only considering the first record WARN 16:05:12,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92987200, only considering the first record WARN 16:05:12,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92987200, only considering the first record WARN 16:05:12,265 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:92987200, only considering the first record WARN 16:05:12,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93065136, only considering the first record WARN 16:05:12,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93065136, only considering the first record WARN 16:05:12,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93065136, only considering the first record WARN 16:05:12,323 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93065139, only considering the first record WARN 16:05:12,324 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93065139, only considering the first record WARN 16:05:12,324 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93065139, only considering the first record WARN 16:05:12,343 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93066968, only considering the first record WARN 16:05:12,343 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93066968, only considering the first record WARN 16:05:12,533 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089882, only considering the first record WARN 16:05:12,533 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089882, only considering the first record WARN 16:05:12,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089882, only considering the first record WARN 16:05:12,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089884, only considering the first record WARN 16:05:12,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089884, only considering the first record WARN 16:05:12,534 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089884, only considering the first record WARN 16:05:12,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089905, only considering the first record WARN 16:05:12,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089905, only considering the first record WARN 16:05:12,535 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93089905, only considering the first record WARN 16:05:12,688 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107273, only considering the first record WARN 16:05:12,689 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107273, only considering the first record WARN 16:05:12,689 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107273, only considering the first record WARN 16:05:12,691 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107534, only considering the first record WARN 16:05:12,691 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107534, only considering the first record WARN 16:05:12,691 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107534, only considering the first record WARN 16:05:12,691 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107537, only considering the first record WARN 16:05:12,692 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107537, only considering the first record WARN 16:05:12,692 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93107537, only considering the first record WARN 16:05:12,726 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93112828, only considering the first record WARN 16:05:12,727 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93112828, only considering the first record WARN 16:05:12,727 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93112828, only considering the first record WARN 16:05:12,731 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93113321, only considering the first record WARN 16:05:12,731 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93113321, only considering the first record WARN 16:05:12,796 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93517901, only considering the first record WARN 16:05:12,796 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93517901, only considering the first record WARN 16:05:12,869 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93539158, only considering the first record WARN 16:05:12,869 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93539158, only considering the first record WARN 16:05:12,881 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93550988, only considering the first record WARN 16:05:12,881 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93550988, only considering the first record WARN 16:05:12,920 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93605682, only considering the first record WARN 16:05:12,920 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93605682, only considering the first record WARN 16:05:12,920 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93605682, only considering the first record WARN 16:05:12,969 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93628167, only considering the first record WARN 16:05:12,969 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93628167, only considering the first record WARN 16:05:12,969 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:93628167, only considering the first record WARN 16:05:13,565 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94036655, only considering the first record WARN 16:05:13,565 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94036655, only considering the first record WARN 16:05:13,566 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94036655, only considering the first record WARN 16:05:14,597 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94051507, only considering the first record WARN 16:05:14,597 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94051507, only considering the first record WARN 16:05:14,912 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94056315, only considering the first record WARN 16:05:14,912 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94056315, only considering the first record WARN 16:05:15,104 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94058420, only considering the first record WARN 16:05:15,105 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94058420, only considering the first record WARN 16:05:15,685 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94285089, only considering the first record WARN 16:05:15,685 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94285089, only considering the first record WARN 16:05:15,924 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94749598, only considering the first record WARN 16:05:15,925 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94749598, only considering the first record WARN 16:05:16,284 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94928523, only considering the first record WARN 16:05:16,285 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94928523, only considering the first record WARN 16:05:16,449 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94944183, only considering the first record WARN 16:05:16,449 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94944183, only considering the first record INFO 16:05:18,258 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.IllegalArgumentException: -1 does not represent a valid base character at org.broadinstitute.gatk.utils.genotyper.DiploidGenotype.createDiploidGenotype(DiploidGenotype.java:115) at org.broadinstitute.gatk.tools.walkers.genotyper.SNPGenotypeLikelihoodsCalculationModel.getLikelihoods(SNPGenotypeLikelihoodsCalculationModel.java:177) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoods(UnifiedGenotypingEngine.java:305) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateLikelihoodsAndGenotypes(UnifiedGenotypingEngine.java:189) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:367) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyper.map(UnifiedGenotyper.java:143) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) 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: -1 does not represent a valid base character ##### ERROR ------------------------------------------------------------------------------------------