INFO 06:34:41,404 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:34:41,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02 INFO 06:34:41,411 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 06:34:41,411 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 06:34:41,414 HelpFormatter - Program Args: -I 14972_realigned.bam -I 14973_realigned.bam -R /Users/thompsoni/gatk/ucsc.hg19.fasta -T UnifiedGenotyper -o twins.UG.vcf -nt 12 -stand_emit_conf 10.0 -stand_call_conf 30.0 --dbsnp /Users/thompsoni/gatk/dbsnp_137.hg19.vcf -glm BOTH -dcov 200 INFO 06:34:41,415 HelpFormatter - Date/Time: 2013/05/20 06:34:41 INFO 06:34:41,415 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:34:41,415 HelpFormatter - -------------------------------------------------------------------------------- INFO 06:34:41,448 ArgumentTypeDescriptor - Dynamically determined type of /Users/thompsoni/gatk/dbsnp_137.hg19.vcf to be VCF INFO 06:34:41,580 GenomeAnalysisEngine - Strictness is SILENT INFO 06:34:41,660 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 200 INFO 06:34:41,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:34:41,688 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 06:34:41,699 RMDTrackBuilder - Creating Tribble index in memory for file /Users/thompsoni/gatk/dbsnp_137.hg19.vcf INFO 06:38:01,508 RMDTrackBuilder - Writing Tribble index to disk for file /Users/thompsoni/gatk/dbsnp_137.hg19.vcf.idx INFO 06:38:20,936 MicroScheduler - Running the GATK in parallel mode with 12 total threads, 1 CPU thread(s) for each of 12 data thread(s), of 24 processors available on this machine INFO 06:38:21,082 GenomeAnalysisEngine - Creating shard strategy for 2 BAM files INFO 06:38:21,708 GenomeAnalysisEngine - Done creating shard strategy INFO 06:38:21,708 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 06:38:21,708 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 06:38:21,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,843 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 INFO 06:38:21,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,908 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 06:38:21,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,923 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,924 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,939 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 06:38:21,940 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:21,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 06:38:21,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12 INFO 06:38:22,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12 INFO 06:38:22,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17 INFO 06:38:22,611 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 06:38:22,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09 INFO 06:38:51,715 ProgressMeter - Starting 0.00e+00 30.0 s 49.6 w 100.0% 30.0 s 0.0 s INFO 06:39:21,719 ProgressMeter - Starting 0.00e+00 60.0 s 99.2 w 100.0% 60.0 s 0.0 s INFO 06:39:51,724 ProgressMeter - Starting 0.00e+00 90.0 s 148.8 w 100.0% 90.0 s 0.0 s INFO 06:40:21,728 ProgressMeter - Starting 0.00e+00 120.0 s 198.4 w 100.0% 120.0 s 0.0 s INFO 06:40:51,732 ProgressMeter - Starting 0.00e+00 2.5 m 248.1 w 100.0% 2.5 m 0.0 s INFO 06:41:21,735 ProgressMeter - Starting 0.00e+00 3.0 m 297.7 w 100.0% 3.0 m 0.0 s INFO 06:41:51,739 ProgressMeter - Starting 0.00e+00 3.5 m 347.3 w 100.0% 3.5 m 0.0 s INFO 06:42:21,743 ProgressMeter - Starting 0.00e+00 4.0 m 396.9 w 100.0% 4.0 m 0.0 s INFO 06:42:51,748 ProgressMeter - Starting 0.00e+00 4.5 m 446.5 w 100.0% 4.5 m 0.0 s INFO 06:43:21,751 ProgressMeter - Starting 0.00e+00 5.0 m 496.1 w 100.0% 5.0 m 0.0 s INFO 06:43:51,755 ProgressMeter - Starting 0.00e+00 5.5 m 545.7 w 100.0% 5.5 m 0.0 s INFO 06:44:21,759 ProgressMeter - Starting 0.00e+00 6.0 m 595.3 w 100.0% 6.0 m 0.0 s INFO 06:44:51,763 ProgressMeter - Starting 0.00e+00 6.5 m 644.9 w 100.0% 6.5 m 0.0 s INFO 06:45:21,768 ProgressMeter - Starting 0.00e+00 7.0 m 694.5 w 100.0% 7.0 m 0.0 s INFO 06:45:51,772 ProgressMeter - Starting 0.00e+00 7.5 m 744.2 w 100.0% 7.5 m 0.0 s INFO 06:46:21,776 ProgressMeter - Starting 0.00e+00 8.0 m 793.8 w 100.0% 8.0 m 0.0 s INFO 06:46:51,783 ProgressMeter - Starting 0.00e+00 8.5 m 843.4 w 100.0% 8.5 m 0.0 s INFO 06:47:21,787 ProgressMeter - Starting 0.00e+00 9.0 m 893.0 w 100.0% 9.0 m 0.0 s INFO 06:47:51,794 ProgressMeter - Starting 0.00e+00 9.5 m 942.6 w 100.0% 9.5 m 0.0 s INFO 06:48:21,797 ProgressMeter - Starting 0.00e+00 10.0 m 992.2 w 100.0% 10.0 m 0.0 s INFO 06:48:51,802 ProgressMeter - Starting 0.00e+00 10.5 m 1041.8 w 100.0% 10.5 m 0.0 s INFO 06:49:21,806 ProgressMeter - Starting 0.00e+00 11.0 m 1091.4 w 100.0% 11.0 m 0.0 s INFO 06:49:51,810 ProgressMeter - Starting 0.00e+00 11.5 m 1141.0 w 100.0% 11.5 m 0.0 s INFO 06:50:21,813 ProgressMeter - Starting 0.00e+00 12.0 m 1190.7 w 100.0% 12.0 m 0.0 s INFO 06:50:51,818 ProgressMeter - Starting 0.00e+00 12.5 m 1240.3 w 100.0% 12.5 m 0.0 s INFO 06:51:21,822 ProgressMeter - Starting 0.00e+00 13.0 m 1289.9 w 100.0% 13.0 m 0.0 s INFO 06:51:51,826 ProgressMeter - Starting 0.00e+00 13.5 m 1339.5 w 100.0% 13.5 m 0.0 s INFO 06:52:21,831 ProgressMeter - Starting 0.00e+00 14.0 m 1389.1 w 100.0% 14.0 m 0.0 s INFO 06:52:51,835 ProgressMeter - Starting 0.00e+00 14.5 m 1438.7 w 100.0% 14.5 m 0.0 s INFO 06:53:21,839 ProgressMeter - Starting 0.00e+00 15.0 m 1488.3 w 100.0% 15.0 m 0.0 s INFO 06:53:51,843 ProgressMeter - Starting 0.00e+00 15.5 m 1537.9 w 100.0% 15.5 m 0.0 s INFO 06:54:21,857 ProgressMeter - Starting 0.00e+00 16.0 m 1587.5 w 100.0% 16.0 m 0.0 s INFO 06:54:51,860 ProgressMeter - Starting 0.00e+00 16.5 m 1637.2 w 100.0% 16.5 m 0.0 s INFO 06:55:21,865 ProgressMeter - Starting 0.00e+00 17.0 m 1686.8 w 100.0% 17.0 m 0.0 s INFO 06:55:51,869 ProgressMeter - Starting 0.00e+00 17.5 m 1736.4 w 100.0% 17.5 m 0.0 s INFO 06:56:21,873 ProgressMeter - Starting 0.00e+00 18.0 m 1786.0 w 100.0% 18.0 m 0.0 s INFO 06:56:51,877 ProgressMeter - Starting 0.00e+00 18.5 m 1835.6 w 100.0% 18.5 m 0.0 s INFO 06:57:21,882 ProgressMeter - Starting 0.00e+00 19.0 m 1885.2 w 100.0% 19.0 m 0.0 s INFO 06:57:51,886 ProgressMeter - Starting 0.00e+00 19.5 m 1934.8 w 100.0% 19.5 m 0.0 s INFO 06:58:21,890 ProgressMeter - Starting 0.00e+00 20.0 m 1984.4 w 100.0% 20.0 m 0.0 s INFO 06:58:51,894 ProgressMeter - Starting 0.00e+00 20.5 m 2034.0 w 100.0% 20.5 m 0.0 s INFO 06:59:21,898 ProgressMeter - Starting 0.00e+00 21.0 m 2083.6 w 100.0% 21.0 m 0.0 s INFO 06:59:51,902 ProgressMeter - Starting 0.00e+00 21.5 m 2133.3 w 100.0% 21.5 m 0.0 s INFO 07:00:21,906 ProgressMeter - Starting 0.00e+00 22.0 m 2182.9 w 100.0% 22.0 m 0.0 s INFO 07:00:51,910 ProgressMeter - Starting 0.00e+00 22.5 m 2232.5 w 100.0% 22.5 m 0.0 s INFO 07:01:21,913 ProgressMeter - Starting 0.00e+00 23.0 m 2282.1 w 100.0% 23.0 m 0.0 s INFO 07:01:51,917 ProgressMeter - Starting 0.00e+00 23.5 m 2331.7 w 100.0% 23.5 m 0.0 s INFO 07:02:21,921 ProgressMeter - Starting 0.00e+00 24.0 m 2381.3 w 100.0% 24.0 m 0.0 s INFO 07:02:51,929 ProgressMeter - Starting 0.00e+00 24.5 m 2430.9 w 100.0% 24.5 m 0.0 s INFO 07:03:21,933 ProgressMeter - Starting 0.00e+00 25.0 m 2480.5 w 100.0% 25.0 m 0.0 s INFO 07:03:51,937 ProgressMeter - Starting 0.00e+00 25.5 m 2530.1 w 100.0% 25.5 m 0.0 s INFO 07:04:21,941 ProgressMeter - Starting 0.00e+00 26.0 m 2579.7 w 100.0% 26.0 m 0.0 s INFO 07:04:51,945 ProgressMeter - Starting 0.00e+00 26.5 m 2629.4 w 100.0% 26.5 m 0.0 s INFO 07:05:15,341 ProgressMeter - done 0.00e+00 26.9 m 2668.0 w 100.0% 26.9 m 0.0 s INFO 07:05:15,341 ProgressMeter - Total runtime 1613.63 secs, 26.89 min, 0.45 hours INFO 07:05:15,429 MicroScheduler - 1148 reads were filtered out during traversal out of 561526 total (0.20%) INFO 07:05:15,429 MicroScheduler - -> 1148 reads (0.20% of total) failing DuplicateReadFilter INFO 07:05:17,930 GATKRunReport - Uploaded run statistics report to AWS S3