Using GATK jar /opt/conda/envs/nf-core-sarek-2.7.1/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-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 /opt/conda/envs/nf-core-sarek-2.7.1/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar ApplyBQSR --help USAGE: ApplyBQSR [arguments] Apply a linear base quality recalibration model trained with the BaseRecalibrator tool. Version:4.1.7.0 Required Arguments: --bqsr-recal-file,-bqsr:File Input recalibration table for BQSR Required. --input,-I:String BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required. --output,-O:String Write output to this file 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} --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} --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} --emit-original-quals:Boolean Emit original base qualities under the OQ tag 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. --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: . --global-qscore-prior:Double Global Qscore Bayesian prior to use for BQSR Default value: -1.0. --help,-h:Boolean display the help message 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. --lenient,-LE:Boolean Lenient processing of VCF files Default value: false. Possible values: {true, false} --preserve-qscores-less-than:Integer Don't recalibrate bases with quality scores less than this threshold Default value: 6. --quantize-quals:Integer Quantize quality scores to a given number of levels Default value: 0. Cannot be used in conjuction with argument(s) staticQuantizationQuals roundDown --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} --reference,-R:GATKPathSpecifier Reference sequence Default value: null. --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} --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null. --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} --use-original-qualities,-OQ:Boolean Use the base quality scores from the OQ tag 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-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} --round-down-quantized:BooleanRound quals down to nearest quantized qual Default value: false. Possible values: {true, false} Cannot be used in conjuction with argument(s) quantizationLevels --showHidden,-showHidden:Boolean display hidden arguments Default value: false. Possible values: {true, false} --static-quantized-quals:Integer Use static quantized quality scores to a given number of levels (with -bqsr) This argument may be specified 0 or more times. Default value: null. Cannot be used in conjuction with argument(s) quantizationLevels 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 Tool returned: 0