INFO 17:40:59,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22 INFO 17:40:59,308 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:40:59,308 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 17:40:59,312 HelpFormatter - Program Args: -R /home/scratch/ngs/simon/arctic/references/hs.build37.1.fa -I 68BL.recal.bam -T HaplotypeCaller -L express_regions.bed --interval_padding 100 -ERC GVCF --variant_index_type LINEAR --variant_index_parameter 128000 --dbsnp /home/antique/pr_99009/people/simon/brescia/project/RESOURCES/All.vcf.gz -o 68BL.recal.rawg.vcf -stand_call_conf 30.0 -stand_emit_conf 10.0 -bamout test3.hc.bam --bamWriterType CALLED_HAPLOTYPES INFO 17:40:59,316 HelpFormatter - Executing as salling@padawan.cbs.dtu.dk on Linux 2.6.37.6-0.11-desktop amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_71-b14. INFO 17:40:59,316 HelpFormatter - Date/Time: 2014/12/01 17:40:59 INFO 17:40:59,316 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:59,316 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:40:59,921 GenomeAnalysisEngine - Strictness is SILENT INFO 17:40:59,965 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 17:40:59,972 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 17:40:59,985 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 17:40:59,991 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 17:41:00,241 IntervalUtils - Processing 1332149 bp from intervals WARN 17:41:00,244 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation INFO 17:41:00,299 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 17:41:00,371 GenomeAnalysisEngine - Done preparing for traversal INFO 17:41:00,372 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 17:41:00,372 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 17:41:00,373 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 17:41:00,374 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output INFO 17:41:00,374 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output INFO 17:41:00,477 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units Using SSE4.1 accelerated implementation of PairHMM INFO 17:41:01,807 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file INFO 17:41:01,807 VectorLoglessPairHMM - Using vectorized implementation of PairHMM INFO 17:41:30,376 ProgressMeter - 1:6278173 118040.0 30.0 s 4.2 m 1.4% 36.9 m 36.4 m INFO 17:42:00,377 ProgressMeter - 1:50940828 204200.0 60.0 s 4.9 m 1.7% 57.3 m 56.3 m INFO 17:42:30,378 ProgressMeter - 1:51171890 541601.0 90.0 s 2.8 m 2.4% 61.3 m 59.8 m INFO 17:43:00,379 ProgressMeter - 1:61742836 1468470.0 120.0 s 81.0 s 3.6% 55.4 m 53.4 m INFO 17:43:30,380 ProgressMeter - 1:112314199 1933595.0 2.5 m 77.0 s 4.2% 59.6 m 57.1 m INFO 17:44:00,381 ProgressMeter - 1:116260224 2524666.0 3.0 m 71.0 s 5.2% 57.9 m 54.9 m INFO 17:44:30,382 ProgressMeter - 1:154671176 3343983.0 3.5 m 62.0 s 6.1% 57.0 m 53.5 m INFO 17:45:00,383 ProgressMeter - 1:154677217 3343983.0 4.0 m 71.0 s 6.6% 60.7 m 56.7 m INFO 17:45:30,384 ProgressMeter - 1:154679935 3343983.0 4.5 m 80.0 s 6.8% 66.2 m 61.7 m INFO 17:46:00,385 ProgressMeter - 1:156052318 4812470.0 5.0 m 62.0 s 7.9% 63.4 m 58.4 m INFO 17:46:30,386 ProgressMeter - 1:156104407 5808873.0 5.5 m 56.0 s 8.7% 63.1 m 57.6 m INFO 17:47:00,387 ProgressMeter - 1:156109767 5808873.0 6.0 m 61.0 s 9.1% 65.8 m 59.8 m INFO 17:47:30,388 ProgressMeter - 1:170700107 8826240.0 6.5 m 44.0 s 10.7% 60.8 m 54.3 m WARN 17:47:40,424 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:170705685 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument INFO 17:48:00,389 ProgressMeter - 1:233765038 9263000.0 7.0 m 45.0 s 11.1% 63.2 m 56.2 m INFO 17:48:30,390 ProgressMeter - 1:233785934 9564088.0 7.5 m 47.0 s 11.4% 65.8 m 58.3 m INFO 17:49:00,391 ProgressMeter - 1:237618035 1.311606E7 8.0 m 36.0 s 12.8% 62.5 m 54.5 m INFO 17:49:30,392 ProgressMeter - 1:237757030 1.612317E7 8.5 m 31.0 s 13.8% 61.4 m 52.9 m INFO 17:50:00,394 ProgressMeter - 1:237843926 2.1192884E7 9.0 m 25.0 s 15.5% 58.2 m 49.2 m INFO 17:50:30,395 ProgressMeter - 1:237920002 2.5254019E7 9.5 m 22.0 s 16.6% 57.2 m 47.7 m INFO 17:51:00,396 ProgressMeter - 1:237961618 2.8664246E7 10.0 m 20.0 s 17.6% 56.8 m 46.8 m