INFO 17:22:12,579 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:22:12,581 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-1-gab2121b, Compiled 2015/07/28 11:32:46 INFO 17:22:12,582 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 17:22:12,582 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 17:22:12,586 HelpFormatter - Program Args: -l INFO -T GenotypeGVCFs -R /net/NGSanalysis/ref/Mus_musculus.GRCm38/index/bwa/Mus_musculus.GRCm38.dna.primary_assembly.fa -o test_gatk3_4_haplotype.vcf -ploidy 2 --max_alternate_alleles 20 --dbsnp /net/NGSanalysis/ref/Mus_musculus.GRCm38/snp/mgp.v5.merged.snps_all.dbSNP142.vcf.gz --num_threads 32 -V:3460_24_K26_ACACAGAA_L002_tjmrb_SPE,VCF 3460_24_K26_ACACAGAA_L002_tjmrb_SPE.g.vcf.gz -V:3460_23_K25_AAGGTACA_L002_tjmrb_SPE,VCF 3460_23_K25_AAGGTACA_L002_tjmrb_SPE.g.vcf.gz INFO 17:22:17,603 HelpFormatter - Executing as roel@utonium.nki.nl on Linux 2.6.32-504.12.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15. INFO 17:22:17,604 HelpFormatter - Date/Time: 2015/07/28 17:22:12 INFO 17:22:17,605 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:22:17,605 HelpFormatter - -------------------------------------------------------------------------------- INFO 17:22:18,132 GenomeAnalysisEngine - Strictness is SILENT INFO 17:22:18,325 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 WARN 17:22:18,836 IndexDictionaryUtils - Track 3460_24_K26_ACACAGAA_L002_tjmrb_SPE doesn't have a sequence dictionary built in, skipping dictionary validation WARN 17:22:18,837 IndexDictionaryUtils - Track 3460_23_K25_AAGGTACA_L002_tjmrb_SPE doesn't have a sequence dictionary built in, skipping dictionary validation WARN 17:22:18,837 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation INFO 17:22:18,847 MicroScheduler - Running the GATK in parallel mode with 32 total threads, 1 CPU thread(s) for each of 32 data thread(s), of 64 processors available on this machine INFO 17:22:18,907 GenomeAnalysisEngine - Preparing for traversal INFO 17:22:18,924 GenomeAnalysisEngine - Done preparing for traversal INFO 17:22:18,925 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 17:22:18,925 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 17:22:18,926 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 17:22:19,041 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.IllegalStateException: Key AD found in VariantContext field FORMAT at 1:28776317 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default. at htsjdk.variant.vcf.VCFEncoder.fieldIsMissingFromHeaderError(VCFEncoder.java:176) at htsjdk.variant.vcf.VCFEncoder.encode(VCFEncoder.java:132) at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:222) at org.broadinstitute.gatk.engine.io.storage.VariantContextWriterStorage.add(VariantContextWriterStorage.java:182) at org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub.add(VariantContextWriterStub.java:271) at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.reduce(GenotypeGVCFs.java:414) at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.reduce(GenotypeGVCFs.java:128) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:291) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociReduce.apply(TraverseLociNano.java:280) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:279) 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.ShardTraverser.call(ShardTraverser.java:98) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.4-1-gab2121b): ##### 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: Key AD found in VariantContext field FORMAT at 1:28776317 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default. ##### ERROR ------------------------------------------------------------------------------------------