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FilterFuncotations Error, ShouldNeverReachHereException, FuncotationMap
This request was created from a contribution made by Joyce Anon on April 25, 2022 06:30 UTC.
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FilterFuncotations stops with an error. The input file with the reference genome seems to pass ValidateVariants (no errors). It looks like "FuncotationMap" doesn't have enough values to go with the keys. I started with a .vcf file downloaded from Nebula Genomics, and sequentially used CNNScoreVariants, FilterVariantTranches (CNN_1D), and Funcotator, with default settings.
I am trying to find the most pathogenic variants. I considered using FilterVcf to remove synonymous and intron variants, but it doesn't look like it can do that. So then I tried FilterFuncotations, but it returns an error. What I want is some way to sort the variants by severity, to find the most pathogenic ones, but I don't know how to do that.
GATK version: 4.2.6.1
Java runtime: OpenJDK 64-Bit Server VM v11.0.14.1+1-Ubuntu-0ubuntu1.20.04
Excerpt:
[April 25, 2022 at 2:00:35 AM EDT] org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=319815680
org.broadinstitute.hellbender.exceptions.GATKException$ShouldNeverReachHereException: Cannot parse the funcotation attribute. Num values: 31 Num keys: 53
Copied from the terminal:
(gatk) aru@BioinformaticsVM:/mnt/sdb/gatk$ ./gatk FilterFuncotations --allele-frequency-data-source gnomad -O ./output/nebulaFilterFuncotations.vcf --ref-version hg38 -V ./output/nebulaFuncotatorAnnotated.vcf --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true'
Using GATK jar /mnt/sdb/gatk/gatk-package-4.2.6.1-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 /mnt/sdb/gatk/gatk-package-4.2.6.1-local.jar FilterFuncotations --allele-frequency-data-source gnomad -O ./output/nebulaFilterFuncotations.vcf --ref-version hg38 -V ./output/nebulaFuncotatorAnnotated.vcf
02:00:34.173 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/sdb/gatk/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
02:00:34.368 INFO FilterFuncotations - ------------------------------------------------------------
02:00:34.369 INFO FilterFuncotations - The Genome Analysis Toolkit (GATK) v4.2.6.1
02:00:34.369 INFO FilterFuncotations - For support and documentation go to https://software.broadinstitute.org/gatk/
02:00:34.369 INFO FilterFuncotations - Executing as aru@BioinformaticsVM on Linux v5.13.0-39-generic amd64
02:00:34.369 INFO FilterFuncotations - Java runtime: OpenJDK 64-Bit Server VM v11.0.14.1+1-Ubuntu-0ubuntu1.20.04
02:00:34.369 INFO FilterFuncotations - Start Date/Time: April 25, 2022 at 2:00:34 AM EDT
02:00:34.369 INFO FilterFuncotations - ------------------------------------------------------------
02:00:34.369 INFO FilterFuncotations - ------------------------------------------------------------
02:00:34.370 INFO FilterFuncotations - HTSJDK Version: 2.24.1
02:00:34.371 INFO FilterFuncotations - Picard Version: 2.27.1
02:00:34.371 INFO FilterFuncotations - Built for Spark Version: 2.4.5
02:00:34.371 INFO FilterFuncotations - HTSJDK Defaults.COMPRESSION_LEVEL : 2
02:00:34.371 INFO FilterFuncotations - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
02:00:34.371 INFO FilterFuncotations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
02:00:34.371 INFO FilterFuncotations - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
02:00:34.371 INFO FilterFuncotations - Deflater: IntelDeflater
02:00:34.371 INFO FilterFuncotations - Inflater: IntelInflater
02:00:34.371 INFO FilterFuncotations - GCS max retries/reopens: 20
02:00:34.371 INFO FilterFuncotations - Requester pays: disabled
02:00:34.372 WARN FilterFuncotations -
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning: FilterFuncotations is an EXPERIMENTAL tool and should not be used for production
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
02:00:34.372 INFO FilterFuncotations - Initializing engine
02:00:34.518 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/sdb/gatk/./output/nebulaFuncotatorAnnotated.vcf
02:00:34.815 INFO FilterFuncotations - Done initializing engine
02:00:35.260 INFO ProgressMeter - Starting traversal
02:00:35.261 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
02:00:35.262 INFO FilterFuncotations - Starting pass 0 through the variants
02:00:35.778 ERROR FuncotationMap - Keys: Gencode_34_hugoSymbol, Gencode_34_ncbiBuild, Gencode_34_chromosome, Gencode_34_start, Gencode_34_end, Gencode_34_variantClassification, Gencode_34_secondaryVariantClassification, Gencode_34_variantType, Gencode_34_refAllele, Gencode_34_tumorSeqAllele1, Gencode_34_tumorSeqAllele2, Gencode_34_genomeChange, Gencode_34_annotationTranscript, Gencode_34_transcriptStrand, Gencode_34_transcriptExon, Gencode_34_transcriptPos, Gencode_34_cDnaChange, Gencode_34_codonChange, Gencode_34_proteinChange, Gencode_34_gcContent, Gencode_34_referenceContext, Gencode_34_otherTranscripts, ACMGLMMLof_LOF_Mechanism, ACMGLMMLof_Mode_of_Inheritance, ACMGLMMLof_Notes, ACMG_recommendation_Disease_Name, ClinVar_VCF_AF_ESP, ClinVar_VCF_AF_EXAC, ClinVar_VCF_AF_TGP, ClinVar_VCF_ALLELEID, ClinVar_VCF_CLNDISDB, ClinVar_VCF_CLNDISDBINCL, ClinVar_VCF_CLNDN, ClinVar_VCF_CLNDNINCL, ClinVar_VCF_CLNHGVS, ClinVar_VCF_CLNREVSTAT, ClinVar_VCF_CLNSIG, ClinVar_VCF_CLNSIGCONF, ClinVar_VCF_CLNSIGINCL, ClinVar_VCF_CLNVC, ClinVar_VCF_CLNVCSO, ClinVar_VCF_CLNVI, ClinVar_VCF_DBVARID, ClinVar_VCF_GENEINFO, ClinVar_VCF_MC, ClinVar_VCF_ORIGIN, ClinVar_VCF_RS, ClinVar_VCF_SSR, ClinVar_VCF_ID, ClinVar_VCF_FILTER, LMMKnown_LMM_FLAGGED, LMMKnown_ID, LMMKnown_FILTER
02:00:35.778 ERROR FuncotationMap - Values: , , , , , , , , , , , , , , , , , , , , , , , , , , , , false, ,
02:00:35.793 INFO FilterFuncotations - Shutting down engine
[April 25, 2022 at 2:00:35 AM EDT] org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=319815680
org.broadinstitute.hellbender.exceptions.GATKException$ShouldNeverReachHereException: Cannot parse the funcotation attribute. Num values: 31 Num keys: 53
at org.broadinstitute.hellbender.tools.funcotator.FuncotationMap.createAsAllTableFuncotationsFromVcf(FuncotationMap.java:224)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.lambda$createAlleleToFuncotationMapFromFuncotationVcfAttribute$5(FuncotatorUtils.java:2256)
at java.base/java.util.stream.Collectors.lambda$uniqKeysMapAccumulator$1(Collectors.java:178)
at java.base/java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
at java.base/java.util.stream.IntPipeline$1$1.accept(IntPipeline.java:180)
at java.base/java.util.stream.Streams$RangeIntSpliterator.forEachRemaining(Streams.java:104)
at java.base/java.util.Spliterator$OfInt.forEachRemaining(Spliterator.java:699)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578)
at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.createAlleleToFuncotationMapFromFuncotationVcfAttribute(FuncotatorUtils.java:2255)
at org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter.buildArHetByGene(ArHetvarFilter.java:77)
at org.broadinstitute.hellbender.tools.funcotator.filtrationRules.ArHetvarFilter.firstPassApply(ArHetvarFilter.java:50)
at org.broadinstitute.hellbender.tools.funcotator.FilterFuncotations.firstPassApply(FilterFuncotations.java:161)
at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.nthPassApply(TwoPassVariantWalker.java:17)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverse$0(MultiplePassVariantWalker.java:40)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverseVariants$1(MultiplePassVariantWalker.java:77)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$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:497)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverseVariants(MultiplePassVariantWalker.java:75)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:40)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
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)
(created from Zendesk ticket #282401)
gz#282401
@GATKSupportTeam Can you ask the user to provide an example FUNCOTATION attribute from their VCF? This error indicates that one or more of the FUNCOTATION attributes are malformed, so it would help to be able to inspect one.
The user's uploaded data is named Joyce1NebulaFuncotatorAnnotated.vcf and Joyce1NebulaFuncotatorAnnotated.vcf.idx.