GenotypeGVCFs error; A USER ERROR has occurred: use-new-qual-calculator is not a recognized option

Hello Terra, 

I am running JointCalling on Whole Exome samples using clone of this workflow 

however the GenotypeGVCFs tasks keeps failing with this error in all the shards; `A USER ERROR has occurred: use-new-qual-calculator is not a recognized option`

I have tried these approaches so far but they all failed to resolve the issue; throwing the same error as above

1.  commenting out (--use-new-qual-calculator) in the GenotypeGVCFs task of wdl

--use-new-qual-calculator

--only-output-calls-starting-in-intervals

2. setting to `false` these parameters in GenotypeGVCFs task

--use-new-qual-calculator false

--only-output-calls-starting-in-intervals false

3.  removing parameters (--only-output-calls-starting-in-intervals and --use-new-qual-calculator) from the command in GenotypeGVCFs task of  wdl

any suggestions on how i could resolve this?

I've attached the stderr for your perusal

thanks

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.cb5f9316
USAGE: GenotypeGVCFs [arguments]

Perform joint genotyping on a single-sample GVCF from HaplotypeCaller or a multi-sample GVCF from CombineGVCFs or
GenomicsDBImport
Version:4.1.6.0


Required Arguments:

--output,-O:File              File to which variants should be written  Required. 

--reference,-R:String         Reference sequence file  Required. 

--variant,-V:String           A VCF file containing variants  Required. 


Optional Arguments:

--add-output-sam-program-record,-add-output-sam-program-record:Boolean
                              If true, adds a PG tag to created SAM/BAM/CRAM files.  Default value: true. Possible
                              values: {true, false} 

--add-output-vcf-command-line,-add-output-vcf-command-line:Boolean
                              If true, adds a command line header line to created VCF files.  Default value: true.
                              Possible values: {true, false} 

--allele-fraction-error:DoubleMargin of error in allele fraction to consider a somatic variant homoplasmic  Default
                              value: 0.001. 

--annotate-with-num-discovered-alleles:Boolean
                              If provided, we will annotate records with the number of alternate alleles that were
                              discovered (but not necessarily genotyped) at a given site  Default value: false. Possible
                              values: {true, false} 

--annotation,-A:String        One or more specific annotations to add to variant calls  This argument may be specified 0
                              or more times. Default value: null. Possible Values: {AlleleFraction,
                              AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
                              AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
                              AS_StrandOddsRatio, BaseQuality, BaseQualityHistogram, BaseQualityRankSumTest,
                              ChromosomeCounts, ClippingRankSumTest, CountNs, Coverage, DepthPerAlleleBySample,
                              DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength, GenotypeSummaries,
                              InbreedingCoeff, LikelihoodRankSumTest, MappingQuality, MappingQualityRankSumTest,
                              MappingQualityZero, OrientationBiasReadCounts, OriginalAlignment, PossibleDeNovo,
                              QualByDepth, ReadPosition, ReadPosRankSumTest, ReferenceBases, RMSMappingQuality,
                              SampleList, StrandBiasBySample, StrandOddsRatio, TandemRepeat, UniqueAltReadCount}

--annotation-group,-G:String  One or more groups of annotations to apply to variant calls  This argument may be
                              specified 0 or more times. Default value: null. Possible Values:
                              {AlleleSpecificAnnotation, AS_StandardAnnotation, ReducibleAnnotation, StandardAnnotation,
                              StandardHCAnnotation, StandardMutectAnnotation}

--annotations-to-exclude,-AX:String
                              One or more specific annotations to exclude from variant calls  This argument may be
                              specified 0 or more times. Default value: null. Possible Values: {BaseQualityRankSumTest,
                              ChromosomeCounts, Coverage, DepthPerAlleleBySample, ExcessHet, FisherStrand,
                              InbreedingCoeff, MappingQualityRankSumTest, QualByDepth, ReadPosRankSumTest,
                              RMSMappingQuality, StrandOddsRatio}

--arguments_file:File         read one or more arguments files and add them to the command line  This argument may be
                              specified 0 or more times. Default value: null. 

--cloud-index-prefetch-buffer,-CIPB:Integer
                              Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
                              cloudPrefetchBuffer if unset.  Default value: -1. 

--cloud-prefetch-buffer,-CPB:Integer
                              Size of the cloud-only prefetch buffer (in MB; 0 to disable).  Default value: 40. 

--create-output-bam-index,-OBI:Boolean
                              If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.  Default
                              value: true. Possible values: {true, false} 

--create-output-bam-md5,-OBM:Boolean
                              If true, create a MD5 digest for any BAM/SAM/CRAM file created  Default value: false.
                              Possible values: {true, false} 

--create-output-variant-index,-OVI:Boolean
                              If true, create a VCF index when writing a coordinate-sorted VCF file.  Default value:
                              true. Possible values: {true, false} 

--create-output-variant-md5,-OVM:Boolean
                              If true, create a a MD5 digest any VCF file created.  Default value: false. Possible
                              values: {true, false} 

--dbsnp,-D:FeatureInput       dbSNP file  Default value: null. 

--disable-bam-index-caching,-DBIC:Boolean
                              If true, don't cache bam indexes, this will reduce memory requirements but may harm
                              performance if many intervals are specified.  Caching is automatically disabled if there
                              are no intervals specified.  Default value: false. Possible values: {true, false} 

--disable-read-filter,-DF:String
                              Read filters to be disabled before analysis  This argument may be specified 0 or more
                              times. Default value: null. Possible Values: {WellformedReadFilter}

--disable-sequence-dictionary-validation,-disable-sequence-dictionary-validation:Boolean
                              If specified, do not check the sequence dictionaries from our inputs for compatibility.
                              Use at your own risk!  Default value: false. Possible values: {true, false} 

--exclude-intervals,-XL:StringOne or more genomic intervals to exclude from processing  This argument may be specified 0
                              or more times. Default value: null. 

--force-output-intervals:String
                              sites at which to output genotypes even if non-variant in samples  This argument may be
                              specified 0 or more times. Default value: null. 

--founder-id,-founder-id:String
                              Samples representing the population "founders"  This argument may be specified 0 or more
                              times. Default value: null. 

--gatk-config-file:String     A configuration file to use with the GATK.  Default value: null. 

--gcs-max-retries,-gcs-retries:Integer
                              If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
                              connection  Default value: 20. 

--gcs-project-for-requester-pays:String
                              Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
                              accessed.  Default value: . 

--help,-h:Boolean             display the help message  Default value: false. Possible values: {true, false} 

--heterozygosity:Double       Heterozygosity value used to compute prior likelihoods for any locus.  See the GATKDocs
                              for full details on the meaning of this population genetics concept  Default value: 0.001.

--heterozygosity-stdev:Double Standard deviation of heterozygosity for SNP and indel calling.  Default value: 0.01. 

--include-non-variant-sites,-all-sites:Boolean
                              Include loci found to be non-variant after genotyping  Default value: false. Possible
                              values: {true, false} 

--indel-heterozygosity:Double Heterozygosity for indel calling.  See the GATKDocs for heterozygosity for full details on
                              the meaning of this population genetics concept  Default value: 1.25E-4. 

--input,-I:String             BAM/SAM/CRAM file containing reads  This argument may be specified 0 or more times.
                              Default value: null. 

--input-is-somatic:Boolean    Finalize input GVCF according to somatic (i.e. Mutect2) TLODs (BETA feature)  Default
                              value: false. Possible values: {true, false} 

--interval-exclusion-padding,-ixp:Integer
                              Amount of padding (in bp) to add to each interval you are excluding.  Default value: 0. 

--interval-merging-rule,-imr:IntervalMergingRule
                              Interval merging rule for abutting intervals  Default value: ALL. Possible values: {ALL,
                              OVERLAPPING_ONLY} 

--interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including.  Default value: 0. 

--interval-set-rule,-isr:IntervalSetRule
                              Set merging approach to use for combining interval inputs  Default value: UNION. Possible
                              values: {UNION, INTERSECTION} 

--intervals,-L:String         One or more genomic intervals over which to operate  This argument may be specified 0 or
                              more times. Default value: null. 

--keep-combined-raw-annotations,-keep-combined:Boolean
                              If specified, keep the combined raw annotations  Default value: false. Possible values:
                              {true, false} 

--lenient,-LE:Boolean         Lenient processing of VCF files  Default value: false. Possible values: {true, false} 

--merge-input-intervals,-merge-input-intervals:Boolean
                              Boolean flag to import all data in between intervals.  Default value: false. Possible
                              values: {true, false} 

--num-reference-samples-if-no-call:Integer
                              Number of hom-ref genotypes to infer at sites not present in a panel  Default value: 0. 

--pedigree,-ped:File          Pedigree file for determining the population "founders"  Default value: null. 

--population-callset,-population:FeatureInput
                              Callset to use in calculating genotype priors  Default value: null. 

--QUIET:Boolean               Whether to suppress job-summary info on System.err.  Default value: false. Possible
                              values: {true, false} 

--read-filter,-RF:String      Read filters to be applied before analysis  This argument may be specified 0 or more
                              times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter,
                              AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
                              FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter,
                              HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter,
                              MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
                              MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
                              MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
                              MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
                              NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
                              NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
                              NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
                              NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
                              OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
                              PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
                              ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter,
                              ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter,
                              ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter,
                              SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter,
                              WellformedReadFilter}

--read-index,-read-index:String
                              Indices to use for the read inputs. If specified, an index must be provided for every read
                              input and in the same order as the read inputs. If this argument is not specified, the
                              path to the index for each input will be inferred automatically.  This argument may be
                              specified 0 or more times. Default value: null. 

--read-validation-stringency,-VS:ValidationStringency
                              Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default
                              stringency value SILENT can improve performance when processing a BAM file in which
                              variable-length data (read, qualities, tags) do not otherwise need to be decoded.  Default
                              value: SILENT. Possible values: {STRICT, LENIENT, SILENT} 

--sample-ploidy,-ploidy:Integer
                              Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in
                              each pool * Sample Ploidy).  Default value: 2. 

--seconds-between-progress-updates,-seconds-between-progress-updates:Double
                              Output traversal statistics every time this many seconds elapse  Default value: 10.0. 

--sequence-dictionary,-sequence-dictionary:String
                              Use the given sequence dictionary as the master/canonical sequence dictionary.  Must be a
                              .dict file.  Default value: null. 

--sites-only-vcf-output:Boolean
                              If true, don't emit genotype fields when writing vcf file output.  Default value: false.
                              Possible values: {true, false} 

--standard-min-confidence-threshold-for-calling,-stand-call-conf:Double
                              The minimum phred-scaled confidence threshold at which variants should be called  Default
                              value: 30.0. 

--tmp-dir:GATKPathSpecifier   Temp directory to use.  Default value: null. 

--tumor-lod-to-emit,-emit-lod:Double
                              LOD threshold to emit variant to VCF.  Default value: 3.5. 

--use-jdk-deflater,-jdk-deflater:Boolean
                              Whether to use the JdkDeflater (as opposed to IntelDeflater)  Default value: false.
                              Possible values: {true, false} 

--use-jdk-inflater,-jdk-inflater:Boolean
                              Whether to use the JdkInflater (as opposed to IntelInflater)  Default value: false.
                              Possible values: {true, false} 

--verbosity,-verbosity:LogLevel
                              Control verbosity of logging.  Default value: INFO. Possible values: {ERROR, WARNING,
                              INFO, DEBUG} 

--version:Boolean             display the version number for this tool  Default value: false. Possible values: {true,
                              false} 


Advanced Arguments:

--disable-tool-default-annotations,-disable-tool-default-annotations:Boolean
                              Disable all tool default annotations  Default value: false. Possible values: {true, false}

--disable-tool-default-read-filters,-disable-tool-default-read-filters:Boolean
                              Disable all tool default read filters (WARNING: many tools will not function correctly
                              without their default read filters on)  Default value: false. Possible values: {true,
                              false} 

--enable-all-annotations:Boolean
                              Use all possible annotations (not for the faint of heart)  Default value: false. Possible
                              values: {true, false} 

--genomicsdb-use-vcf-codec:Boolean
                              Use VCF Codec Streaming for data from GenomicsDB instead of the default BCF  Default
                              value: false. Possible values: {true, false} 

--max-alternate-alleles:Integer
                              Maximum number of alternate alleles to genotype  Default value: 6. 

--max-genotype-count:Integer  Maximum number of genotypes to consider at any site  Default value: 1024. 

--only-output-calls-starting-in-intervals:Boolean
                              Restrict variant output to sites that start within provided intervals  Default value:
                              false. Possible values: {true, false} 

--showHidden,-showHidden:Boolean
                              display hidden arguments  Default value: false. Possible values: {true, false} 

Conditional Arguments for annotation:

Valid only if "RMSMappingQuality" is specified:
--allow-old-rms-mapping-quality-annotation-data:Boolean
                              Override to allow old RMSMappingQuality annotated VCFs to function  Default value: false.
                              Possible values: {true, false} 

Conditional Arguments for readFilter:

Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases:Integer  Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
                              overrides threshold fraction.  Default value: null.  Cannot be used in conjuction with
                              argument(s) maxAmbiguousBaseFraction

--ambig-filter-frac:Double    Threshold fraction of ambiguous bases  Default value: 0.05.  Cannot be used in conjuction
                              with argument(s) maxAmbiguousBases

Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length:Integer Maximum length of fragment (insert size)  Default value: 1000000. 

--min-fragment-length:Integer Minimum length of fragment (insert size)  Default value: 0. 

Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals:String       One or more genomic intervals to keep  This argument must be specified at least once.
                              Required. 

Valid only if "LibraryReadFilter" is specified:
--library,-library:String     Name of the library to keep  This argument must be specified at least once. Required. 

Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality:Integer
                              Maximum mapping quality to keep (inclusive)  Default value: null. 

--minimum-mapping-quality:Integer
                              Minimum mapping quality to keep (inclusive)  Default value: 10. 

Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length:Integer
                              Minimum start location difference at which mapped mates are considered distant  Default
                              value: 1000. 

Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends:Boolean
                              Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
                              both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
                              block  Default value: false. Possible values: {true, false} 

--filter-too-short:Integer    Minimum number of aligned bases  Default value: 30. 

Valid only if "PlatformReadFilter" is specified:
--platform-filter-name:String Platform attribute (PL) to match  This argument must be specified at least once. Required.

Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes:String   Platform unit (PU) to filter out  This argument must be specified at least once. Required.

Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list:StringA read group filter expression in the form "attribute:value", where "attribute" is a two
                              character read group attribute such as "RG" or "PU".  This argument must be specified at
                              least once. Required. 

Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group:String      The name of the read group to keep  Required. 

Valid only if "ReadLengthReadFilter" is specified:
--max-read-length:Integer     Keep only reads with length at most equal to the specified value  Required. 

--min-read-length:Integer     Keep only reads with length at least equal to the specified value  Default value: 1. 

Valid only if "ReadNameReadFilter" is specified:
--read-name:String            Keep only reads with this read name  Required. 

Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only:Boolean
                              Keep only reads on the reverse strand  Required. Possible values: {true, false} 

Valid only if "SampleReadFilter" is specified:
--sample,-sample:String       The name of the sample(s) to keep, filtering out all others  This argument must be
                              specified at least once. Required. 

Valid only if "SoftClippedReadFilter" is specified:
--invert-soft-clip-ratio-filter:Boolean
                              Inverts the results from this filter, causing all variants that would pass to fail and
                              visa-versa.  Default value: false. Possible values: {true, false} 

--soft-clipped-leading-trailing-ratio:Double
                              Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
                              in read for read to be filtered.  Default value: null.  Cannot be used in conjuction with
                              argument(s) minimumSoftClippedRatio

--soft-clipped-ratio-threshold:Double
                              Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
                              read for read to be filtered.  Default value: null.  Cannot be used in conjuction with
                              argument(s) minimumLeadingTrailingSoftClippedRatio


***********************************************************************

A USER ERROR has occurred: use-new-qual-calculator is not a recognized option

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.1.6.0-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 -Xms8g -jar /gatk/gatk-package-4.1.6.0-local.jar GenotypeGVCFs -R /cromwell_root/genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.fasta -O Germline_SampleSet_4Haplotype_caller.0.vcf.gz -D gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf -G StandardAnnotation -G AS_StandardAnnotation --only-output-calls-starting-in-intervals false --use-new-qual-calculator false -V gendb://genomicsdb -L gs://fc-1f2cec15-4c83-4842-8fde-c79a1131b2dd/6b8186e3-282f-46f9-a798-803e5cd7a5b7/JointGenotyping/dca116c7-2029-4354-a2b6-70b3380ab4aa/call-SplitIntervalList/cacheCopy/glob-d928cd0f5fb17b6bd5e635f48c18ccfb/0000-scattered.interval_list --merge-input-intervals