Hello, 

I am running into issues with my VariantFiltration step that stops without completing. It appears to work just fine and is able to identify 5 snps in the output file (all from the first 6 rows of unfiltered snps), but then it doesn't filter any more of the remain data. The log says "Shutting down engine" and then lists a problem with Java "java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Boolean." I haven't been able to find any other posts about this particular issue. I did try running this with multiple versions (4.2.6.1, 4.2.2.0 and 4.1.4.1). I've copied here the log and command used. I've been following along this pipeline (https://github.com/lindsawi/HybSeq-SNP-Extraction). 

Thanks so much for all your help!

a) GATK version used: 4.2.6.1, 4.2.2.0 and 4.1.4.1
b) Exact command used: VariantFiltration -R rorida_quinquenervia_supercontig_reference.fasta -V Rorida_quinquenervia.SNPall.vcf --filter-name hardfilter -O Rorida_quinquenervia.snp.filtered.vcf --filter-expression QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0
c) Entire program log:

Using GATK jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/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 -jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar CombineGVCFs -R rorida_quinquenervia_supercontig_reference.fasta --variant samples.list --output Rorida_quinquenervia.cohort.g.vcf
12:50:08.108 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:50:08.405 INFO  CombineGVCFs - ------------------------------------------------------------
12:50:08.405 INFO  CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.2.6.1
12:50:08.405 INFO  CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
12:50:08.408 INFO  CombineGVCFs - Executing as theresa.saunders@cn136.mgmt.kamiak.wsu.edu on Linux v3.10.0-693.11.6.el7.x86_64 amd64
12:50:08.408 INFO  CombineGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_92-b14
12:50:08.409 INFO  CombineGVCFs - Start Date/Time: September 9, 2022 12:50:08 PM PDT
12:50:08.409 INFO  CombineGVCFs - ------------------------------------------------------------
12:50:08.409 INFO  CombineGVCFs - ------------------------------------------------------------
12:50:08.409 INFO  CombineGVCFs - HTSJDK Version: 2.24.1
12:50:08.409 INFO  CombineGVCFs - Picard Version: 2.27.1
12:50:08.409 INFO  CombineGVCFs - Built for Spark Version: 2.4.5
12:50:08.409 INFO  CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:50:08.409 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:50:08.410 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:50:08.410 INFO  CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:50:08.410 INFO  CombineGVCFs - Deflater: IntelDeflater
12:50:08.410 INFO  CombineGVCFs - Inflater: IntelInflater
12:50:08.410 INFO  CombineGVCFs - GCS max retries/reopens: 20
12:50:08.410 INFO  CombineGVCFs - Requester pays: disabled
12:50:08.410 INFO  CombineGVCFs - Initializing engine
12:50:09.016 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/158_Rorida_quinquenervia_%3Ffimbriata-g.vcf
12:50:09.086 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/159_Rorida_quinquenervia_%3Fnoeana-g.vcf
12:50:09.145 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/160_Rorida_quinquenervia_%3Fnoeana-g.vcf
12:50:09.235 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/161_Rorida_quinquenervia_%3Fnoeana_brachystyla-g.vcf
12:50:09.290 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/44_Rorida_quinquenervia_%3Fdolichostyla-g.vcf
12:50:09.317 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/96_Rorida_quinquenervia_%3Fdolichostyla-g.vcf
12:50:11.927 INFO  CombineGVCFs - Done initializing engine
12:50:12.070 INFO  ProgressMeter - Starting traversal
12:50:12.070 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
12:50:12.270 WARN  ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location 4471_supercontig_158:130 the annotation MLEAC=[0, 0] was not a numerical value and was ignored
12:50:22.447 INFO  ProgressMeter - 5257_supercontig_158:522              0.2                 29000         167694.7
12:50:32.493 INFO  ProgressMeter - 5454_supercontig_158:545              0.3                 60000         176271.9
12:50:42.495 INFO  ProgressMeter - 6226_supercontig_158:957              0.5                155000         305669.7
12:50:48.363 INFO  ProgressMeter - 7602_supercontig_158:932              0.6                249914         413160.7
12:50:48.363 INFO  ProgressMeter - Traversal complete. Processed 249914 total variants in 0.6 minutes.
12:50:48.483 INFO  CombineGVCFs - Shutting down engine
[September 9, 2022 12:50:48 PM PDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.67 minutes.
Runtime.totalMemory()=2675441664
Using GATK jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/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 -jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GenotypeGVCFs -R rorida_quinquenervia_supercontig_reference.fasta -V Rorida_quinquenervia.cohort.g.vcf -O Rorida_quinquenervia.cohort.unfiltered.vcf
12:50:56.573 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:50:57.110 INFO  GenotypeGVCFs - ------------------------------------------------------------
12:50:57.111 INFO  GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.2.6.1
12:50:57.111 INFO  GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
12:50:57.140 INFO  GenotypeGVCFs - Executing as theresa.saunders@cn136.mgmt.kamiak.wsu.edu on Linux v3.10.0-693.11.6.el7.x86_64 amd64
12:50:57.140 INFO  GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_92-b14
12:50:57.140 INFO  GenotypeGVCFs - Start Date/Time: September 9, 2022 12:50:56 PM PDT
12:50:57.140 INFO  GenotypeGVCFs - ------------------------------------------------------------
12:50:57.140 INFO  GenotypeGVCFs - ------------------------------------------------------------
12:50:57.141 INFO  GenotypeGVCFs - HTSJDK Version: 2.24.1
12:50:57.141 INFO  GenotypeGVCFs - Picard Version: 2.27.1
12:50:57.141 INFO  GenotypeGVCFs - Built for Spark Version: 2.4.5
12:50:57.141 INFO  GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:50:57.141 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:50:57.141 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:50:57.141 INFO  GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:50:57.141 INFO  GenotypeGVCFs - Deflater: IntelDeflater
12:50:57.141 INFO  GenotypeGVCFs - Inflater: IntelInflater
12:50:57.141 INFO  GenotypeGVCFs - GCS max retries/reopens: 20
12:50:57.141 INFO  GenotypeGVCFs - Requester pays: disabled
12:50:57.141 INFO  GenotypeGVCFs - Initializing engine
12:50:57.727 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/Rorida_quinquenervia.cohort.g.vcf
12:50:57.925 INFO  GenotypeGVCFs - Done initializing engine
12:50:58.029 INFO  ProgressMeter - Starting traversal
12:50:58.029 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
12:50:58.382 WARN  InbreedingCoeff - InbreedingCoeff will not be calculated at position 4471_supercontig_158:146 and possibly subsequent; at least 10 samples must have called genotypes
12:51:08.034 INFO  ProgressMeter - 6265_supercontig_158:1253              0.2                106000         635745.7
12:51:09.608 INFO  ProgressMeter - 7628_supercontig_158:690              0.2                168073         870919.8
12:51:09.608 INFO  ProgressMeter - Traversal complete. Processed 168073 total variants in 0.2 minutes.
12:51:09.616 INFO  GenotypeGVCFs - Shutting down engine
[September 9, 2022 12:51:09 PM PDT] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=2960654336
Using GATK jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/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 -jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar SelectVariants -V Rorida_quinquenervia.cohort.unfiltered.vcf -R rorida_quinquenervia_supercontig_reference.fasta -select-type-to-include SNP -O Rorida_quinquenervia.SNPall.vcf
12:51:12.214 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:51:12.358 INFO  SelectVariants - ------------------------------------------------------------
12:51:12.358 INFO  SelectVariants - The Genome Analysis Toolkit (GATK) v4.2.6.1
12:51:12.358 INFO  SelectVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
12:51:12.359 INFO  SelectVariants - Executing as theresa.saunders@cn136 on Linux v3.10.0-693.11.6.el7.x86_64 amd64
12:51:12.359 INFO  SelectVariants - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_92-b14
12:51:12.359 INFO  SelectVariants - Start Date/Time: September 9, 2022 12:51:12 PM PDT
12:51:12.359 INFO  SelectVariants - ------------------------------------------------------------
12:51:12.359 INFO  SelectVariants - ------------------------------------------------------------
12:51:12.359 INFO  SelectVariants - HTSJDK Version: 2.24.1
12:51:12.359 INFO  SelectVariants - Picard Version: 2.27.1
12:51:12.359 INFO  SelectVariants - Built for Spark Version: 2.4.5
12:51:12.359 INFO  SelectVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:51:12.360 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:51:12.360 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:51:12.360 INFO  SelectVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:51:12.360 INFO  SelectVariants - Deflater: IntelDeflater
12:51:12.360 INFO  SelectVariants - Inflater: IntelInflater
12:51:12.360 INFO  SelectVariants - GCS max retries/reopens: 20
12:51:12.360 INFO  SelectVariants - Requester pays: disabled
12:51:12.360 INFO  SelectVariants - Initializing engine
12:51:12.805 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/Rorida_quinquenervia.cohort.unfiltered.vcf
12:51:12.844 INFO  SelectVariants - Done initializing engine
12:51:12.881 INFO  ProgressMeter - Starting traversal
12:51:12.882 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
12:51:13.157 INFO  ProgressMeter - 6933_supercontig_158:481              0.0                  9808        2147737.2
12:51:13.157 INFO  ProgressMeter - Traversal complete. Processed 9808 total variants in 0.0 minutes.
12:51:13.163 INFO  SelectVariants - Shutting down engine
[September 9, 2022 12:51:13 PM PDT] org.broadinstitute.hellbender.tools.walkers.variantutils.SelectVariants done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=2140143616

real    0m3.679s
user    0m9.330s
sys    0m0.801s
Using GATK jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/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 -jar /weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar VariantFiltration -R rorida_quinquenervia_supercontig_reference.fasta -V Rorida_quinquenervia.SNPall.vcf --filter-name hardfilter -O Rorida_quinquenervia.snp.filtered.vcf --filter-expression QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0
12:51:15.887 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/weka/apps/gatk/4.2.6.1/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:51:16.030 INFO  VariantFiltration - ------------------------------------------------------------
12:51:16.031 INFO  VariantFiltration - The Genome Analysis Toolkit (GATK) v4.2.6.1
12:51:16.031 INFO  VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
12:51:16.031 INFO  VariantFiltration - Executing as theresa.saunders@cn136 on Linux v3.10.0-693.11.6.el7.x86_64 amd64
12:51:16.031 INFO  VariantFiltration - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_92-b14
12:51:16.031 INFO  VariantFiltration - Start Date/Time: September 9, 2022 12:51:15 PM PDT
12:51:16.031 INFO  VariantFiltration - ------------------------------------------------------------
12:51:16.031 INFO  VariantFiltration - ------------------------------------------------------------
12:51:16.032 INFO  VariantFiltration - HTSJDK Version: 2.24.1
12:51:16.032 INFO  VariantFiltration - Picard Version: 2.27.1
12:51:16.032 INFO  VariantFiltration - Built for Spark Version: 2.4.5
12:51:16.032 INFO  VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:51:16.032 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:51:16.032 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:51:16.032 INFO  VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:51:16.032 INFO  VariantFiltration - Deflater: IntelDeflater
12:51:16.032 INFO  VariantFiltration - Inflater: IntelInflater
12:51:16.032 INFO  VariantFiltration - GCS max retries/reopens: 20
12:51:16.032 INFO  VariantFiltration - Requester pays: disabled
12:51:16.032 INFO  VariantFiltration - Initializing engine
12:51:16.482 INFO  FeatureManager - Using codec VCFCodec to read file file:///weka/data/lab/roalson/cleomaceae/slimp_snps/round_1_and_2_and_kew_cola_filtered_brassicales_filtered_paralogs_min_and_filtering/rorida_quinquenervia/Rorida_quinquenervia.SNPall.vcf
12:51:16.525 INFO  VariantFiltration - Done initializing engine
12:51:16.592 INFO  ProgressMeter - Starting traversal
12:51:16.592 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
12:51:16.613 WARN  JexlEngine - ![35,44]: 'QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0;' undefined variable MQRankSum
12:51:16.615 WARN  JexlEngine - ![35,44]: 'QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0;' undefined variable MQRankSum
12:51:16.616 WARN  JexlEngine - ![35,44]: 'QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0;' undefined variable MQRankSum
12:51:16.616 WARN  JexlEngine - ![35,44]: 'QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0;' undefined variable MQRankSum
12:51:16.616 WARN  JexlEngine - ![35,44]: 'QD < 5.0 & FS > 60.0 & MQ < 40.0 & MQRankSum < -12.5 & ReadPosRankSum < -8.0;' undefined variable MQRankSum
12:51:16.621 INFO  VariantFiltration - Shutting down engine
[September 9, 2022 12:51:16 PM PDT] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2135949312
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Boolean
    at htsjdk.variant.variantcontext.JEXLMap.evaluateExpression(JEXLMap.java:186)
    at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:95)
    at htsjdk.variant.variantcontext.JEXLMap.get(JEXLMap.java:15)
    at htsjdk.variant.variantcontext.VariantContextUtils.match(VariantContextUtils.java:338)
    at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.matchesFilter(VariantFiltration.java:452)
    at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.filter(VariantFiltration.java:406)
    at org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration.apply(VariantFiltration.java:353)
    at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
    at java.util.stream.ForEachOps$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.VariantWalker.traverse(VariantWalker.java:102)
    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)

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