INFO 10:30:19,426 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:30:19,429 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 INFO 10:30:19,429 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 10:30:19,430 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 10:30:19,434 HelpFormatter - Program Args: -T UnifiedGenotyper -R /PUBLIC_DATA/GENERATED/GenomeRef/chr_chrom_1kg_human_h37.fasta -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -stand_call_conf 0.0 -glm BOTH -G none -rf BadCigar -o sortie.vcf -alleles A.B.recode.vcf -L A.B.recode.vcf -I A.B.bam INFO 10:30:19,440 HelpFormatter - Executing as sletort@Lanascol on Linux 3.2.0-52-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. INFO 10:30:19,440 HelpFormatter - Date/Time: 2014/08/21 10:30:19 INFO 10:30:19,441 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:30:19,441 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:30:19,566 GenomeAnalysisEngine - Strictness is SILENT INFO 10:30:19,694 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 10:30:19,704 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 10:30:19,719 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 10:30:19,888 RMDTrackBuilder - Writing Tribble index to disk for file /WORKING_DIRECTORY/sletort/support_équipe/MultiSample/by_chrom/chrom7/93.55M.95M/A.B.recode.vcf.idx INFO 10:30:20,490 IntervalUtils - Processing 762 bp from intervals INFO 10:30:20,568 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 10:30:20,617 GenomeAnalysisEngine - Done preparing for traversal INFO 10:30:20,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 10:30:20,618 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 10:30:20,618 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime WARN 10:30:21,090 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94749598, only considering the first record WARN 10:30:21,091 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94749598, only considering the first record WARN 10:30:22,655 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94928523, only considering the first record WARN 10:30:22,655 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94928523, only considering the first record WARN 10:30:23,057 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94944183, only considering the first record WARN 10:30:23,058 GenotypingGivenAllelesUtils - Multiple valid VCF records detected in the alleles input file at site chr7:94944183, only considering the first record INFO 10:30:24,451 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 ------------------------------------------------------------------------------------------