If you are seeing an error, please provide(REQUIRED) :
a) GATK version used:

GATK 4.1.9.0

b) Exact command used:

gatk BaseRecalibrator -R /b37/human_g1k_v37.fasta.gz -I sample_mdup_corrected.bam -known-sites /b37/dbsnp_138.b37.vcf -known-sites /b37/Mills_and_1000G_gold_standard.indels.b37.vcf -O sample_recal_data.table

c) Entire error log:

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/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar BaseRecalibrator -R /b37/human_g1k_v37.fasta.gz -I sample_mdup_corrected.bam -known-sites /b37/dbsnp_138.b37.vcf -known-sites /b37/Mills_and_1000G_gold_standard.indels.b37.vcf -O sample_recal_data.table
15:15:23.503 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 17, 2020 3:15:23 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
15:15:23.589 INFO BaseRecalibrator - ------------------------------------------------------------
15:15:23.589 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.9.0
15:15:23.589 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
15:15:23.589 INFO BaseRecalibrator - Executing as user@user-hp-elitedesk-800-g4-wks-twr on Linux v4.15.0-128-generic amd64
15:15:23.589 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_275-8u275-b01-0ubuntu1~16.04-b01
15:15:23.589 INFO BaseRecalibrator - Start Date/Time: December 17, 2020 3:15:23 PM KST
15:15:23.589 INFO BaseRecalibrator - ------------------------------------------------------------
15:15:23.589 INFO BaseRecalibrator - ------------------------------------------------------------
15:15:23.590 INFO BaseRecalibrator - HTSJDK Version: 2.23.0
15:15:23.590 INFO BaseRecalibrator - Picard Version: 2.23.3
15:15:23.590 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:15:23.590 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:15:23.590 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:15:23.590 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:15:23.590 INFO BaseRecalibrator - Deflater: IntelDeflater
15:15:23.590 INFO BaseRecalibrator - Inflater: IntelInflater
15:15:23.590 INFO BaseRecalibrator - GCS max retries/reopens: 20
15:15:23.590 INFO BaseRecalibrator - Requester pays: disabled
15:15:23.590 INFO BaseRecalibrator - Initializing engine
15:15:23.802 INFO FeatureManager - Using codec VCFCodec to read file file:///storage/b37/dbsnp_138.b37.vcf
15:15:23.870 INFO FeatureManager - Using codec VCFCodec to read file file:///storage/b37/Mills_and_1000G_gold_standard.indels.b37.vcf
15:15:23.890 INFO BaseRecalibrator - Done initializing engine
15:15:23.893 INFO BaseRecalibrationEngine - The covariates being used here:
15:15:23.893 INFO BaseRecalibrationEngine - ReadGroupCovariate
15:15:23.893 INFO BaseRecalibrationEngine - QualityScoreCovariate
15:15:23.893 INFO BaseRecalibrationEngine - ContextCovariate
15:15:23.893 INFO BaseRecalibrationEngine - CycleCovariate
15:15:23.897 INFO ProgressMeter - Starting traversal
15:15:23.897 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute
15:15:23.932 INFO BaseRecalibrator - Shutting down engine
[December 17, 2020 3:15:23 PM KST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1196949504
java.lang.ArrayIndexOutOfBoundsException: -118
at org.broadinstitute.hellbender.utils.BaseUtils.convertIUPACtoN(BaseUtils.java:123)
at org.broadinstitute.hellbender.utils.fasta.CachingIndexedFastaSequenceFile.getSubsequenceAt(CachingIndexedFastaSequenceFile.java:340)
at org.broadinstitute.hellbender.engine.ReferenceFileSource.queryAndPrefetch(ReferenceFileSource.java:78)
at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.calculateIsSNPOrIndel(BaseRecalibrationEngine.java:372)
at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.processRead(BaseRecalibrationEngine.java:131)
at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:191)
at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:96)
at java.util.stream.ForEachOps$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.ReadWalker.traverse(ReadWalker.java:94)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
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)

---------------------------------------------------------------------------------------------

The run finishes with no output table. I could not seem to understand what I'm doing wrong here.

I have run the ValidateSamFile on the input BAM file to check and it showed "No errors found"

I'm using the reference files from GATK resource bundle "b37" and running the latest version of GATK. I followed the Gatk best practice instructions from creating a clean BAM upto the MarkDuplicates step. 

I have searched the forum and other sites for a solve but didn't find anything helpful.

Please help.