REQUIRED for all errors and issues:
a) GATK version used: v4.1.2.0
b) Exact command used: BaseRecalibrator                                                c) Entire program log:

The following have been reloaded with a version change:
  1) Java/1.8.0_212 => Java/11.0.2

15:26:10.753 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/beegfs/easybuild/CentOS/7.6.1810/Skylake/software/GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Oct 27, 2022 3:26:13 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
15:26:13.164 INFO  BaseRecalibrator - ------------------------------------------------------------
15:26:13.165 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.2.0
15:26:13.165 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:26:13.166 INFO  BaseRecalibrator - Executing as jgarcia@node01 on Linux v3.10.0-957.el7.x86_64 amd64
15:26:13.167 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.2+9
15:26:13.168 INFO  BaseRecalibrator - Start Date/Time: October 27, 2022 at 3:26:10 PM CEST
15:26:13.168 INFO  BaseRecalibrator - ------------------------------------------------------------
15:26:13.169 INFO  BaseRecalibrator - ------------------------------------------------------------
15:26:13.195 INFO  BaseRecalibrator - HTSJDK Version: 2.19.0
15:26:13.196 INFO  BaseRecalibrator - Picard Version: 2.19.0
15:26:13.196 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:26:13.197 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:26:13.197 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:26:13.198 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:26:13.198 INFO  BaseRecalibrator - Deflater: IntelDeflater
15:26:13.199 INFO  BaseRecalibrator - Inflater: IntelInflater
15:26:13.200 INFO  BaseRecalibrator - GCS max retries/reopens: 20
15:26:13.200 INFO  BaseRecalibrator - Requester pays: disabled
15:26:13.201 INFO  BaseRecalibrator - Initializing engine
15:26:13.619 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/jgarcia/Grape2/./Initial_variants/Spa1-1a_bqsr_snps.vcf
15:26:13.656 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/jgarcia/Grape2/./Initial_variants/Spa1-1a_bqsr_indels.vcf
15:26:13.686 INFO  BaseRecalibrator - Done initializing engine
15:26:13.690 INFO  BaseRecalibrationEngine - The covariates being used here: 
15:26:13.691 INFO  BaseRecalibrationEngine -     ReadGroupCovariate
15:26:13.692 INFO  BaseRecalibrationEngine -     QualityScoreCovariate
15:26:13.693 INFO  BaseRecalibrationEngine -     ContextCovariate
15:26:13.693 INFO  BaseRecalibrationEngine -     CycleCovariate
15:26:13.707 INFO  ProgressMeter - Starting traversal
15:26:13.708 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:26:13.717 INFO  BaseRecalibrator - Shutting down engine
[October 27, 2022 at 3:26:13 PM CEST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=75169792
Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/hellbender/transformers/ReadTransformer. Method lambda$identity$d67512bf$1(Lorg/broadinstitute/hellbender/utils/read/GATKRead;)Lorg/broadinstitute/hellbender/utils/read/GATKRead; at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
    at org.broadinstitute.hellbender.transformers.ReadTransformer.identity(ReadTransformer.java:30)
    at org.broadinstitute.hellbender.engine.GATKTool.makePreReadFilterTransformer(GATKTool.java:345)
    at org.broadinstitute.hellbender.engine.GATKTool.getTransformedReadStream(GATKTool.java:374)
    at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:93)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
    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:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)
Using GATK jar /beegfs/easybuild/CentOS/7.6.1810/Skylake/software/GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8/gatk-package-4.1.2.0-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 -jar /beegfs/easybuild/CentOS/7.6.1810/Skylake/software/GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8/gatk-package-4.1.2.0-local.jar BaseRecalibrator -reference ./Reference/Vitis_vinifera.PN40024.v4.dna.toplevel.fa -I ./Dedup_reads/Spa1-1a_sorted_dedup.bam --known-sites ./Initial_variants/Spa1

-1a_bqsr_snps.vcf --known-sites ./Initial_variants/Spa1_

-1a_bqsr_indels.vcf -O ./BQSR/Spa1-1a_recal_data.table

I'm having this Java exception: Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/hellbender/transformers/ReadTransformer. Method lambda$identity$d67512bf$1(Lorg/broadinstitute/hellbender/utils/read/GATKRead;)Lorg/broadinstitute/hellbender/utils/read/GATKRead; at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef

I've found similar probelms where this bug was caused by the Java version. I'm trying to use Java/1.8.0_212 but it seems that BaseRecalibrator is changing it:

The following have been reloaded with a version change:
  1) Java/1.8.0_212 => Java/11.0.2

I'm working on a HPC.

There is a way to prevent BaseRecalibrator from change Java version?

Thanks in advance.