Can you please provide
a) GATK version used     

gatk 3.8

b) Exact GATK commands used

java -Xmx4g -jar ../GenomeAnalysisTK.jar \

-T IndelRealigner \

-R $reference_fa_path/GRCh38_full_analysis_set_plus_decoy_hla.fa \

-I $MarkDup_output/$1_BWA_MarkDup.bam \

-known $reference_vcf_path/Homo_sapiens_assembly38.dbsnp138.vcf \

-known $reference_vcf_path/Homo_sapiens_assembly38.known_indels.vcf.gz \

-known $reference_vcf_path/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \

-targetIntervals $Realign_path/$1_realignment_targets.intervals \

--BQSR $recal_path/recal_data.txt \

--bam_compression 1 \

-kpr \

-SQQ 10 -SQQ 20 -SQQ 30 -SQQ 40 \

--preserve_qscores_less_than 6 \

-o $Realign_path/$1_realign.bam

c) The entire error log if applicable.

##### ERROR stack trace
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.Byte
at org.broadinstitute.gatk.engine.recalibration.covariates.QualityScoreCovariate.keyFromValue(QualityScoreCovariate.java:96)
at org.broadinstitute.gatk.engine.recalibration.RecalibrationReport.parseQualityScoreTable(RecalibrationReport.java:209)
at org.broadinstitute.gatk.engine.recalibration.RecalibrationReport.<init>(RecalibrationReport.java:96)
at org.broadinstitute.gatk.engine.recalibration.RecalibrationReport.<init>(RecalibrationReport.java:60)
at org.broadinstitute.gatk.engine.recalibration.BaseRecalibration.<init>(BaseRecalibration.java:77)
at org.broadinstitute.gatk.engine.recalibration.BQSRReadTransformer.initializeSub(BQSRReadTransformer.java:59)
at org.broadinstitute.gatk.engine.iterators.ReadTransformer.initialize(ReadTransformer.java:88)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeReadTransformers(GenomeAnalysisEngine.java:426)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeDataSources(GenomeAnalysisEngine.java:839)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:294)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.8-1-0-gf15c1c3ef):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: java.lang.Long cannot be cast to java.lang.Byte
##### ERROR ------------------------------------------------------------------------------------------

What should I do to solve this problem?