INFO 13:19:34,408 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:19:34,410 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-1-g07a4bf8, Compiled 2014/03/18 06:09:21 INFO 13:19:34,410 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 13:19:34,410 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 13:19:34,413 HelpFormatter - Program Args: -R /home/kstamm/ref/GATK/bundle/1.2//human_g1k_v37.fasta -L -L /data/Common_Lab/WGS/myh6.bed -I [[18 -I and BAMs given]] --alleles /data/Common_Lab/WGS/varSites.vcf --genotyping_mode GENOTYPE_GIVEN_ALLELES -T HaplotypeCaller --dbsnp /data/ref/GATK_bundle/2.8/dbsnp_138.b37.vcf -o 18WGS.HC.vcf INFO 13:19:34,416 HelpFormatter - Executing as kstamm@aristotle.phys.mcw.edu on Linux 2.6.32-431.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_45-mockbuild_2013_11_22_18_30-b00. INFO 13:19:34,416 HelpFormatter - Date/Time: 2014/06/13 13:19:34 INFO 13:19:34,416 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:19:34,417 HelpFormatter - -------------------------------------------------------------------------------- INFO 13:19:34,510 GenomeAnalysisEngine - Strictness is SILENT INFO 13:19:34,592 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 13:19:34,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 13:19:34,666 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07 INFO 13:19:34,676 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 13:19:34,869 RMDTrackBuilder - Writing Tribble index to disk for file /data/Common_Lab/WGS/varSites.vcf.idx INFO 13:19:35,025 IntervalUtils - Processing 30000 bp from intervals INFO 13:19:35,134 GenomeAnalysisEngine - Preparing for traversal over 18 BAM files INFO 13:19:36,166 GenomeAnalysisEngine - Done preparing for traversal INFO 13:19:36,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 13:19:36,166 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining INFO 13:19:36,244 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 13:20:06,169 ProgressMeter - 14:23850734 0.00e+00 30.0 s 49.6 w 2.4% 20.5 m 20.0 m ....snip out 40 minutes / 80 lines .... INFO 14:00:26,271 ProgressMeter - 14:23857874 0.00e+00 40.8 m 4051.1 w 26.2% 2.6 h 114.8 m INFO 14:00:56,272 ProgressMeter - 14:23858268 0.00e+00 41.3 m 4100.7 w 27.6% 2.5 h 108.7 m INFO 14:01:08,338 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.NumberFormatException: For input string: "." at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1241) at java.lang.Double.parseDouble(Double.java:540) at org.broadinstitute.variant.variantcontext.GenotypeLikelihoods.parseDeprecatedGLString(GenotypeLikelihoods.java:253) at org.broadinstitute.variant.variantcontext.GenotypeLikelihoods.fromGLField(GenotypeLikelihoods.java:83) at org.broadinstitute.variant.vcf.AbstractVCFCodec.createGenotypeMap(AbstractVCFCodec.java:689) at org.broadinstitute.variant.vcf.AbstractVCFCodec$LazyVCFGenotypesParser.parse(AbstractVCFCodec.java:113) at org.broadinstitute.variant.variantcontext.LazyGenotypesContext.decode(LazyGenotypesContext.java:131) at org.broadinstitute.variant.variantcontext.LazyGenotypesContext.getGenotypes(LazyGenotypesContext.java:121) at org.broadinstitute.variant.variantcontext.GenotypesContext.iterator(GenotypesContext.java:462) at org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.mergeGenotypes(GATKVariantContextUtils.java:1471) at org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.simpleMerge(GATKVariantContextUtils.java:902) at org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.simpleMerge(GATKVariantContextUtils.java:806) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:189) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:880) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:141) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8): ##### 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: For input string: "." ##### ERROR ------------------------------------------------------------------------------------------