INFO 12:58:59,689 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:58:59,691 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 12:58:59,692 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 12:58:59,692 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 12:58:59,696 HelpFormatter - Program Args: -R /home/scratch/ngs/simon/arctic/references/hs.build37.1.fa -T HaplotypeCaller -I ex.list -L /home/people/salling/Express/express_regions.bed --dbsnp /home/antique/pr_99009/people/simon/brescia/project/RESOURCES/All.vcf.gz -nct 16 -o express.raw.vcf -stand_call_conf 30.0 -stand_emit_conf 10.0 INFO 12:58:59,707 HelpFormatter - Executing as salling@translation on Linux 3.0.101-0.7.17-default amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_71-b14. INFO 12:58:59,707 HelpFormatter - Date/Time: 2014/11/26 12:58:59 INFO 12:58:59,707 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:58:59,708 HelpFormatter - -------------------------------------------------------------------------------- INFO 12:59:00,402 GenomeAnalysisEngine - Strictness is SILENT INFO 12:59:00,620 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 12:59:00,629 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 12:59:02,060 SAMDataSource$SAMReaders - Init 50 BAMs in last 1.43 s, 50 of 86 in 1.43 s / 0.02 m (34.98 tasks/s). 36 remaining with est. completion in 1.03 s / 0.02 m INFO 12:59:02,661 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 2.03 INFO 12:59:03,934 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 12:59:04,250 IntervalUtils - Processing 1049293 bp from intervals WARN 12:59:04,254 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation INFO 12:59:04,332 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 16 CPU thread(s) for each of 1 data thread(s), of 512 processors available on this machine INFO 12:59:04,715 GenomeAnalysisEngine - Preparing for traversal over 86 BAM files INFO 12:59:08,151 GenomeAnalysisEngine - Done preparing for traversal INFO 12:59:08,152 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 12:59:08,152 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 12:59:08,153 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 12:59:08,153 HaplotypeCaller - Disabling physical phasing, which is supported only for reference-model confidence output INFO 12:59:08,267 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 12:59:08,268 PairHMM - Performance profiling for PairHMM is disabled because HaplotypeCaller is being run with multiple threads (-nct>1) option Profiling is enabled only when running in single thread mode INFO 12:59:18,086 VectorLoglessPairHMM - 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