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Official code repository for GATK versions 4 and up
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Key END found in VariantContext field INFO at Gbar_A01:24359 but this key isn't defined in the VCFHeader #7708

Closed qymeng1996 closed 2 years ago

qymeng1996 commented 2 years ago

Hello, I want to merge multi HaplotypeCaller GVCF files into a single GVCF with CombineGVCFs, but I got a error warnings, Key END found in VariantContext field INFO at Gbar_A01:24359 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default. I ran the gatk with 4.1.6 version, here is my command. java -Xmx200g -jar /public/home/qymeng/biosoft/gatk-4.1.6.0/gatk-package-4.1.6.0-local.jar CombineGVCFs -O Gb.gatk.vcf -R /data/cotton/QingyingMeng/Gbarbadese_5Sample/3-79/Ref/Gbarbadense_3-79_HAU_v2.fasta -V Y2003/Y2003.gatk.vcf -V Y2010/Y2010.gatk.vcf -V Y2013/Y2013.gatk.vcf,

I recheck my gvcf files and find the variant in the Y2010.gatk.vcf, which is a delete variant Gbar_A01 24359 . GA G 847.03 . AC=2;AF=1.00;AN=2;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=46.41;QD=27.24;SOR=0.963 GT:AD:DP:GQ:PL 1/1:0,23:23:69:861,69,0

I have no ideal to solve it, did anyone eocounter the same error warnings,

Best wishes, Qingying

And here is my log

21:09:58.763 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/public/home/qymeng/biosoft/gatk-4.1.6.0/gatk-package-4.1.6.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Mar 06, 2022 9:09:59 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 21:09:59.072 INFO CombineGVCFs - ------------------------------------------------------------ 21:09:59.073 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.1.6.0 21:09:59.073 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 21:09:59.073 INFO CombineGVCFs - Executing as qymeng@s004 on Linux v3.10.0-862.el7.x86_64 amd64 21:09:59.073 INFO CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_92-b15 21:09:59.073 INFO CombineGVCFs - Start Date/Time: March 6, 2022 9:09:58 PM CST 21:09:59.073 INFO CombineGVCFs - ------------------------------------------------------------ 21:09:59.073 INFO CombineGVCFs - ------------------------------------------------------------ 21:09:59.074 INFO CombineGVCFs - HTSJDK Version: 2.21.2 21:09:59.074 INFO CombineGVCFs - Picard Version: 2.21.9 21:09:59.074 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 21:09:59.074 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 21:09:59.074 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 21:09:59.074 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 21:09:59.074 INFO CombineGVCFs - Deflater: IntelDeflater 21:09:59.074 INFO CombineGVCFs - Inflater: IntelInflater 21:09:59.074 INFO CombineGVCFs - GCS max retries/reopens: 20 21:09:59.074 INFO CombineGVCFs - Requester pays: disabled 21:09:59.074 INFO CombineGVCFs - Initializing engine 21:09:59.773 INFO FeatureManager - Using codec VCFCodec to read file file:///data/cotton/QingyingMeng/Gbarbadese_5Sample/3-79/02_Haplotype/Y2003/Y2003.gatk.vcf 21:09:59.982 INFO FeatureManager - Using codec VCFCodec to read file file:///data/cotton/QingyingMeng/Gbarbadese_5Sample/3-79/02_Haplotype/Y2010/Y2010.gatk.vcf 21:10:00.200 INFO FeatureManager - Using codec VCFCodec to read file file:///data/cotton/QingyingMeng/Gbarbadese_5Sample/3-79/02_Haplotype/Y2013/Y2013.gatk.vcf 21:10:41.729 INFO CombineGVCFs - Done initializing engine 21:10:41.789 INFO ProgressMeter - Starting traversal 21:10:41.790 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 21:10:42.082 INFO CombineGVCFs - Shutting down engine [March 6, 2022 9:10:42 PM CST] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.73 minutes. Runtime.totalMemory()=4515692544 java.lang.IllegalStateException: Key END found in VariantContext field INFO at Gbar_A01:24359 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:213) at htsjdk.variant.vcf.VCFEncoder.write(VCFEncoder.java:146) at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:250) at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.endPreviousStates(CombineGVCFs.java:408) at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.createIntermediateVariants(CombineGVCFs.java:217) at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.apply(CombineGVCFs.java:162) at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:131) at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:106) at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:120) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Iterator.forEachRemaining(Iterator.java:116) at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:118) at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.traverse(MultiVariantWalkerGroupedOnStart.java:163) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206) at org.broadinstitute.hellbender.Main.main(Main.java:292)

sunjh22 commented 2 years ago

Hi I came across the same issue today, may I know how you solve it?

Thanks