REQUIRED for all errors and issues:
a) GATK version used: 

/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar

b) Exact command used: gatk BaseRecalibrator -I ${aligned_reads}/SRR062634_sorted_dedup_reads.bam -R ${ref} --known-sites ${known_sites} -O ${data}/recal_data.table
c) Entire program log: 

STEP 4: Base quality recalibration

Using GATK jar /home/aaina/apps/gatk-4.5.0.0/gatk-package-4.5.0.0-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 /home/aaina/apps/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar BaseRecalibrator -I /home/aaina/Desktop/demo/VC/aligned_reads/SRR062634_sorted_dedup_reads.bam -R /home/aaina/Desktop/demo/supporting_files/hg38/hg38.fa --known-sites /home/aaina/Desktop/demo/supporting_files/hg38/Homo_sapiens_assembly38.dbsnp138.vcf -O /home/aaina/Desktop/demo/VC/data/recal_data.table

14:45:15.543 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/aaina/apps/gatk-4.5.0.0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

14:45:15.633 INFO  BaseRecalibrator - ------------------------------------------------------------

14:45:15.636 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.5.0.0

14:45:15.636 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/

14:45:15.636 INFO  BaseRecalibrator - Executing as aaina@ellison on Linux v4.18.0-513.11.1.el8_9.x86_64 amd64

14:45:15.636 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v20.0.2-internal-adhoc..src

14:45:15.636 INFO  BaseRecalibrator - Start Date/Time: May 15, 2024, 2:45:15 PM CDT

14:45:15.636 INFO  BaseRecalibrator - ------------------------------------------------------------

14:45:15.636 INFO  BaseRecalibrator - ------------------------------------------------------------

14:45:15.637 INFO  BaseRecalibrator - HTSJDK Version: 4.1.0

14:45:15.637 INFO  BaseRecalibrator - Picard Version: 3.1.1

14:45:15.637 INFO  BaseRecalibrator - Built for Spark Version: 3.5.0

14:45:15.637 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2

14:45:15.637 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

14:45:15.637 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

14:45:15.637 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

14:45:15.638 INFO  BaseRecalibrator - Deflater: IntelDeflater

14:45:15.638 INFO  BaseRecalibrator - Inflater: IntelInflater

14:45:15.638 INFO  BaseRecalibrator - GCS max retries/reopens: 20

14:45:15.638 INFO  BaseRecalibrator - Requester pays: disabled

14:45:15.638 INFO  BaseRecalibrator - Initializing engine

14:45:15.755 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/aaina/Desktop/demo/supporting_files/hg38/Homo_sapiens_assembly38.dbsnp138.vcf

14:45:15.879 INFO  BaseRecalibrator - Shutting down engine

[May 15, 2024, 2:45:15 PM CDT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.

Runtime.totalMemory()=285212672

java.lang.IllegalArgumentException: Something went wrong with sequence dictionary detection, check that reference has a valid sequence dictionary

at org.broadinstitute.hellbender.utils.Utils.nonNull(Utils.java:643)

at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:149)

at org.broadinstitute.hellbender.utils.SequenceDictionaryUtils.validateDictionaries(SequenceDictionaryUtils.java:98)

at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:796)

at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:731)

at org.broadinstitute.hellbender.engine.ReadWalker.onStartup(ReadWalker.java:51)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:147)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)

at org.broadinstitute.hellbender.Main.main(Main.java:306)