Hi GATK team and community,

I've encountered an  java.util.ArrayList cannot be cast to java.lang.String error while trying to run VariantRecalibrator

GATK version used:

4.2.6.1

Exact command used:

gatk --java-options "-Xms63g -XX:+UseParallelGC -XX:ParallelGCThreads=3" \
     VariantRecalibrator \
     -V gs://hgdp-1kg/vqsr_pipeline/gnomad_genomes_v3.1_info.vcf.bgz \
     -O ${BATCH_TMPDIR}/VQSR__SNPsVariantRecalibratorScattered-IXH8P/recalibration \
     --tranches-file ${BATCH_TMPDIR}/VQSR__SNPsVariantRecalibratorScattered-IXH8P/tranches \
     --trust-all-polymorphic \
     -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 \
     -an AS_QD -an AS_MQRankSum -an AS_ReadPosRankSum -an AS_FS -an AS_MQ \
     -mode SNP \
     --max-gaussians 6 \
     -resource:hapmap,known=false,training=true,truth=true,prior=15 gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz \
     -resource:omni,known=false,training=true,truth=true,prior=12 gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz \
     -resource:1000G,known=false,training=true,truth=false,prior=10 gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
     -resource:dbsnp,known=true,training=false,truth=false,prior=7 gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz
     -L ${BATCH_TMPDIR}/Make_1000_intervals-2nqFj/intervals/0000-scattered.interval_list --use-allele-specific-annotations --input-model ${BATCH_TMPDIR}/VQSR__SNPsVariantRecalibratorCreateModel-YClEf/model_file --output-tranches-for-scatter

Entire error log:

19:09:41.070 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
19:09:41.097 INFO  VariantRecalibrator - ------------------------------------------------------------
19:09:41.098 INFO  VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.6.1
19:09:41.098 INFO  VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
19:09:41.098 INFO  VariantRecalibrator - Executing as root@hostname-e3a86afed9 on Linux v5.4.0-1042-gcp amd64
19:09:41.098 INFO  VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
19:09:41.098 INFO  VariantRecalibrator - Start Date/Time: August 29, 2022 7:09:41 PM GMT
19:09:41.098 INFO  VariantRecalibrator - ------------------------------------------------------------
19:09:41.098 INFO  VariantRecalibrator - ------------------------------------------------------------
19:09:41.099 INFO  VariantRecalibrator - HTSJDK Version: 2.24.1
19:09:41.099 INFO  VariantRecalibrator - Picard Version: 2.27.1
19:09:41.099 INFO  VariantRecalibrator - Built for Spark Version: 2.4.5
19:09:41.099 INFO  VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:09:41.099 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:09:41.099 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:09:41.099 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:09:41.099 INFO  VariantRecalibrator - Deflater: IntelDeflater
19:09:41.099 INFO  VariantRecalibrator - Inflater: IntelInflater
19:09:41.099 INFO  VariantRecalibrator - GCS max retries/reopens: 20
19:09:41.099 INFO  VariantRecalibrator - Requester pays: disabled
19:09:41.099 INFO  VariantRecalibrator - Initializing engine
19:09:43.093 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz
19:09:45.614 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz
19:09:48.115 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz
19:09:50.675 INFO  FeatureManager - Using codec VCFCodec to read file gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.gz
19:09:53.628 INFO  FeatureManager - Using codec VCFCodec to read file gs://hgdp-1kg/vqsr_pipeline/gnomad_genomes_v3.1_info.vcf.bgz
19:09:57.965 INFO  VariantRecalibrator - Done initializing engine
19:09:57.968 INFO  TrainingSet - Found hapmap track: 	Known = false 	Training = true 	Truth = true 	Prior = Q15.0
19:09:57.968 INFO  TrainingSet - Found omni track: 	Known = false 	Training = true 	Truth = true 	Prior = Q12.0
19:09:57.968 INFO  TrainingSet - Found 1000G track: 	Known = false 	Training = true 	Truth = false 	Prior = Q10.0
19:09:57.968 INFO  TrainingSet - Found dbsnp track: 	Known = true 	Training = false 	Truth = false 	Prior = Q7.0
19:09:58.022 WARN  GATKVariantContextUtils - Can't determine output variant file format from output file extension "". Defaulting to VCF.
19:09:58.076 INFO  ProgressMeter - Starting traversal
19:09:58.076 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
19:09:58.646 INFO  VariantRecalibrator - Shutting down engine
[August 29, 2022 7:09:59 PM GMT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 0.30 minutes.
Runtime.totalMemory()=64827162624
org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at chr1:10007 [VC gs://hgdp-1kg/vqsr_pipeline/gnomad_genomes_v3.1_info.vcf.bgz @ chr1:10007 Q. of type=SNP alleles=[T*, C] attr={AC=0, AC_raw=1, AS_FS=3.97940, AS_MQ=32.2452, AS_MQRankSum=0.358000, AS_QD=3.60000, AS_QUALapprox=|18, AS_ReadPosRankSum=1.23100, AS_SB_TABLE=[3, 0|1, 1], AS_VarDP=|5, AS_pab_max=1.00000, FS=3.97940, MQ=32.2452, MQRankSum=0.358000, QD=3.60000, QUALapprox=18, ReadPosRankSum=1.23100, SB=[3, 0, 1, 1], VarDP=5} GT=[] filters=
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:145)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
	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:482)
	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.traverse(MultiVariantWalker.java:136)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.lang.ClassCastException: java.util.ArrayList cannot be cast to java.lang.String
	at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsDouble(CommonInfo.java:324)
	at htsjdk.variant.variantcontext.VariantContext.getAttributeAsDouble(VariantContext.java:820)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.decodeAnnotation(VariantDataManager.java:359)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantDataManager.decodeAnnotations(VariantDataManager.java:328)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addDatum(VariantRecalibrator.java:602)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.addVariantDatum(VariantRecalibrator.java:572)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.lambda$consumeQueuedVariants$0(VariantRecalibrator.java:543)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.consumeQueuedVariants(VariantRecalibrator.java:543)
	at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.apply(VariantRecalibrator.java:522)
	at org.broadinstitute.hellbender.engine.MultiVariantWalker.lambda$traverse$1(MultiVariantWalker.java:139)
	... 20 more

Genevieve Brandt (she/her) the previous error I was experiencing has been fixed. This step is the one where we apply the model to each interval.