CombineGVCFs - A USER ERROR has occurred: Bad input: Raw value for annotation has 1 values, expected 2
AnsweredHi everyone,
I tried to run the CombineGVCFs command on GATK v4.1.9.0 and was prompted with the following error message:
A USER ERROR has occurred: Bad input: Raw value for annotation has 1 values, expected 2
Not sure what might be the origin of this error message. Could someone shed some light on the reason why this error occurred?
GATK version used: 4.1.9.0
Exact command used:
/gatk/gatk-4.1.9.0/gatk --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true CombineGVCFs \
-R /REFERENCE/gatk_resourcebunde_GRCH38.fasta \
-O /Databases/xxxx_xxxxxxx_2022.1.vcf.gz \
-V /SQZ/S_053/SQZ_053.g.vcf.gz \
-V /SQZ/S_036/SQZ_036.g.vcf.gz \
-V /SQZ/SQZ_073/SQZ_073.g.vcf.gz \
-V /SQZ/SQZ_185/SQZ_185.g.vcf.gz \
-V /SQZ/S_079/SQZ_079.g.vcf.gz \
-V /SQZ/S_065/SQZ_065.g.vcf.gz
Entire program log:
GVCF Merging execution date: 21-09-2022T18:34:19.008060
18:34:20.370 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Sep 21, 2022 6:34:20 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
18:34:20.454 INFO CombineGVCFs - ------------------------------------------------------------
18:34:20.454 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.1.9.0
18:34:20.454 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
18:34:20.454 INFO CombineGVCFs - Executing as uichuimi@aorus on Linux v5.4.0-125-generic amd64
18:34:20.454 INFO CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v16.0.1+9
18:34:20.455 INFO CombineGVCFs - Start Date/Time: 21 de septiembre de 2022, 18:34:20 WEST
18:34:20.455 INFO CombineGVCFs - ------------------------------------------------------------
18:34:20.455 INFO CombineGVCFs - ------------------------------------------------------------
18:34:20.455 INFO CombineGVCFs - HTSJDK Version: 2.23.0
18:34:20.455 INFO CombineGVCFs - Picard Version: 2.23.3
18:34:20.455 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
18:34:20.455 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
18:34:20.455 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
18:34:20.455 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
18:34:20.455 INFO CombineGVCFs - Deflater: IntelDeflater
18:34:20.455 INFO CombineGVCFs - Inflater: IntelInflater
18:34:20.455 INFO CombineGVCFs - GCS max retries/reopens: 20
18:34:20.455 INFO CombineGVCFs - Requester pays: disabled
18:34:20.455 INFO CombineGVCFs - Initializing engine
18:34:20.718 INFO FeatureManager - Using codec VCFCodec to read file file://GENOMES/SQZ/S_053/SQZ_053.g.vcf.gz
18:34:20.800 INFO FeatureManager - Using codec VCFCodec to read file file://GENOMES/SQZ/S_036/SQZ_036.g.vcf.gz
18:34:20.855 INFO FeatureManager - Using codec VCFCodec to read file file://GENOMES/SQZ/SQZ_073/SQZ_073.g.vcf.gz
18:34:20.935 INFO FeatureManager - Using codec VCFCodec to read file file://GENOMES/SQZ/SQZ_185/SQZ_185.g.vcf.gz
18:34:20.986 INFO FeatureManager - Using codec VCFCodec to read file file://GENOMES/SQZ/S_079/SQZ_079.g.vcf.gz
18:34:21.065 INFO FeatureManager - Using codec VCFCodec to read file file://GENOMES/SQZ/S_065/SQZ_065.g.vcf.gz
18:35:13.951 INFO CombineGVCFs - Done initializing engine
18:35:13.978 INFO ProgressMeter - Starting traversal
18:35:13.979 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
18:35:14.053 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location chr1:10146 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
18:35:23.983 INFO ProgressMeter - chr1:2308680 0.2 962000 5769692.1
18:35:32.865 INFO CombineGVCFs - Shutting down engine
[21 de septiembre de 2022, 18:35:32 WEST] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 1.21 minutes.
Runtime.totalMemory()=629145600
***********************************************************************
A USER ERROR has occurred: Bad input: Raw value for annotation has 1 values, expected 2
***********************************************************************
org.broadinstitute.hellbender.exceptions.UserException$BadInput: Bad input: Raw value for annotation has 1 values, expected 2
at org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality.parseRawDataString(RMSMappingQuality.java:303)
at org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality.parseRawDataString(RMSMappingQuality.java:295)
at org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality.combineRawData(RMSMappingQuality.java:131)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.combineAnnotations(VariantAnnotatorEngine.java:210)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.mergeAttributes(ReferenceConfidenceVariantContextMerger.java:318)
at org.broadinstitute.hellbender.tools.walkers.ReferenceConfidenceVariantContextMerger.merge(ReferenceConfidenceVariantContextMerger.java:142)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.endPreviousStates(CombineGVCFs.java:407)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.createIntermediateVariants(CombineGVCFs.java:221)
at org.broadinstitute.hellbender.tools.walkers.CombineGVCFs.apply(CombineGVCFs.java:166)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:131)
at org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart.apply(MultiVariantWalkerGroupedOnStart.java:106)
at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:120)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:596)
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:1049)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /gatk/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar CombineGVCFs -R /REFERENCE/gatk_resourcebunde_GRCH38.fasta -O /Databases/xxxx_xxxxxxx_2022.1.vcf.gz -V /GENOMES/SQZ/S_053/SQZ_053.g.vcf.gz -V /GENOMES/SQZ/S_036/SQZ_036.g.vcf.gz -V /GENOMES/SQZ/SQZ_073/SQZ_073.g.vcf.gz -V /GENOMES/SQZ/SQZ_185/SQZ_185.g.vcf.gz -V /GENOMES/SQZ/S_079/SQZ_079.g.vcf.gz -V /GENOMES/SQZ/S_065/SQZ_065.g.vcf.gz
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Hi David Medina,
Do you know how these VCFs were created? It looks like there is an issue in your RMSMappingQuality annotation.
Best,
Genevieve
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Hi David,
We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!
Kind regards,
Genevieve
-
Hi,
I am not sure how this VCF was created. I ran the process again and it seemed to solve the problem. However, I would like to know if there was any other plan of action I could apply in order to "fix" the wrong RMSMappingQuality annotations.
Thank you,
David Medina
-
Hi David Medina,
Unfortunately, there isn't a better way to do this. The RMSMappingQuality annotations are annotated by the mapper and cannot be re-annotated in GATK if they are missing.
Best,
Genevieve
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