Hello, below you can see the entire program log after running baserecalibrator where you can see the gatk version and full command ran.

Some background into my project: I have 8 cell cultures from the same individual and hifi reads that went into a reference genome and I am using all of them for snp calling. (performed separate for each sample and joint afterwards) 
Because this is a non-model organism I am using the final snps as a dbSNP and plan to do 3 rounds of recalibration for each individual sample before joint calling one last time. On the first round, right after joint calling I get the log below for all sample types.

The problem is that no matter how much I increase the max cycle the cycle found is always 1 higher than what I use. Why is it? How can I fix it?

Using GATK jar /path/to/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 -Xmx4g -Xms4g -XX:ParallelGCThreads=2 -jar /path/to/gatk/4.2.6.1/gatk-package-4.2.6.1-local.jar BaseRecalibrator -I RESULTS/MAPPED_READS/HIFI/hifi_reads.bam -R /share/pool/CompGenomVert/StrixAssembly/RESULTS/CURATED/ref_genome.inter.fa --known-sites RESULTS/MAPPED_READS/HC/allsites.vcf.gz --maximum-cycle-value 20000 -O RESULTS/CALLED/HIFI/recalibration1/hifi_reads.recalc.table
12:21:41.777 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/path/to/gatk/4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:21:41.896 INFO  BaseRecalibrator - ------------------------------------------------------------
12:21:41.896 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.2.6.1
12:21:41.896 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
12:21:41.896 INFO  BaseRecalibrator - Executing as ychrysostomakis@compute-0-9.local on Linux v3.10.0-1160.105.1.el7.x86_64 amd64
12:21:41.896 INFO  BaseRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_231-b11
12:21:41.897 INFO  BaseRecalibrator - Start Date/Time: 2. August 2024 12:21:41 MESZ
12:21:41.897 INFO  BaseRecalibrator - ------------------------------------------------------------
12:21:41.897 INFO  BaseRecalibrator - ------------------------------------------------------------
12:21:41.897 INFO  BaseRecalibrator - HTSJDK Version: 2.24.1
12:21:41.897 INFO  BaseRecalibrator - Picard Version: 2.27.1
12:21:41.897 INFO  BaseRecalibrator - Built for Spark Version: 2.4.5
12:21:41.897 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:21:41.897 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:21:41.897 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:21:41.897 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:21:41.897 INFO  BaseRecalibrator - Deflater: IntelDeflater
12:21:41.898 INFO  BaseRecalibrator - Inflater: IntelInflater
12:21:41.898 INFO  BaseRecalibrator - GCS max retries/reopens: 20
12:21:41.898 INFO  BaseRecalibrator - Requester pays: disabled
12:21:41.898 INFO  BaseRecalibrator - Initializing engine
12:21:42.276 INFO  FeatureManager - Using codec VCFCodec to read file file:///path/to/RESULTS/MAPPED_READS/HC/allsites.vcf.gz
12:21:42.359 INFO  BaseRecalibrator - Done initializing engine
12:21:42.360 WARN  BaseRecalibrator - This tool has only been well tested on ILLUMINA-based sequencing data. For other data use at your own risk.
12:21:42.362 INFO  BaseRecalibrationEngine - The covariates being used here: 
12:21:42.362 INFO  BaseRecalibrationEngine -     ReadGroupCovariate
12:21:42.362 INFO  BaseRecalibrationEngine -     QualityScoreCovariate
12:21:42.362 INFO  BaseRecalibrationEngine -     ContextCovariate
12:21:42.362 INFO  BaseRecalibrationEngine -     CycleCovariate
12:21:42.374 INFO  ProgressMeter - Starting traversal
12:21:42.374 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
12:21:43.421 INFO  BaseRecalibrator - Shutting down engine
[2. August 2024 12:21:43 MESZ] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=4116185088
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A USER ERROR has occurred: The maximum allowed value for the cycle is 20000, but a larger cycle (20001) was detected.  Please use the --maximum-cycle-value argument (when creating the recalibration table in BaseRecalibrator) to increase this value (at the expense of requiring more memory to run)

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I have the same error regardless of whether I use

--java-options "-Xmx4g -Xms4g -XX:ParallelGCThreads=2"