Error while running gatk

Question

[ashaneev07]

Hiii Can anyone please help me to find a solution for this...I got the following error while running gatk for variant filtering.

home@home-Lenovo-H30-50:~/Documents/Tools_NGS/gatk-4.0.6.0$ ./gatk VariantFiltration \ -R /home/Documents/Tools_NGS/VariantCall/MaSuRCA_hybrid_assembly.fa \  -V /media/veena/TOSHIBAEXT/Variant_Calling/Untitled Folder/snps_300bp.vcf.gz

USAGE: VariantFiltration [arguments]

Filter variant calls based on INFO and/or FORMAT annotations.
Version:4.0.6.0

 Required Arguments:

--output,-O:String            File to which variants should be written  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} 

--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. 

--cluster-size,-cluster:Integer
                              The number of SNPs which make up a cluster. Must be at least 2  Default value: 
--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} 

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

--filter-expression,-filter:String
                              One or more expression used with INFO fields to filter  This argument may be specified 0
                              or more times. Default value: null. 

--filter-name:String          Names to use for the list of filters  This argument may be specified 0 or more times.
                              Default value: null. 

--filter-not-in-mask:Boolean  Filter records NOT in given input mask.  Default value: false. Possible values: {true,
                              false} 

--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. 

--genotype-filter-expression,-G-filter:String
                              One or more expression used with FORMAT (sample/genotype-level) fields to filter (see
                              documentation guide for more info)  This argument may be specified 0 or more times.
                              Default value: null. 

--genotype-filter-name,-G-filter-name:String
                              Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name
                              is put in the FILTER field for variants that get filtered  This argument may be specified
                              0 or more times. Default value: null. 

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

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

--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} 


--invalidate-previous-filters:Boolean
                              Remove previous filters applied to the VCF  Default value: false. Possible values: {true,
                              false} 

--invert-filter-expression,-invfilter:Boolean
                              Invert the selection criteria for --filterExpression  Default value: false. Possible
                              values: {true, false} 

--invert-genotype-filter-expression,-invG-filter:Boolean
                              Invert the selection criteria for --genotypeFilterExpression  Default value: false.
                              Possible values: {true, false} 

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

--mask,-mask:FeatureInput     Input mask  Default value: null. 

--mask-extension:Integer      How many bases beyond records from a provided 'mask' should variants be filtered  Default
                              value: 0. 

--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, LibraryReadFilter, MappedReadFilter,
                              MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
                              MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
                              MateOnSameContigOrNoMappedMateReadFilter, MetricsReadFilter,
                              NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter,
                              NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter,
                              NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter,
                              PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter,
                              PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter,
                              ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
                              ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter,
                              SeqIsStoredReadFilter, 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:String         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. 

--set-filtered-genotype-to-no-call:Boolean
                              Set filtered genotypes to no-call  Default value: false. Possible values: {true, false} 

--sites-only-vcf-output:Boolean
                              If true, don't emit genotype fields when writing vcf file output.  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} 

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

Conditional Arguments for read-filter:

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

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 "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:StringThe name of the read group to filter out  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. 


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

    A USER ERROR has occurred: Invalid argument ' -R'.

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

[finswimmer]

Have you read this in the message?

A USER ERROR has occurred: Invalid argument ' -R'.

fin swimmer

[Bastien Hervé]

Seems to be an acceptable option in the docs

java -jar GenomeAnalysisTK.jar \

-T VariantFiltration \

-R reference.fasta \

-o output.vcf \

--variant input.vcf \

--filterExpression "AB < 0.2 || MQ0 > 50" \

--filterName "SomeFilterName"

[finswimmer]

Hello <uname>,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

In your case the number of allowed chars is exceeded if you trying to do this. For long code or messages it would be better to create a gist on github and just copy and paste the link to it here.

Thank you!

[ashaneev07]

Thanks for your kind response..

[Bastien Hervé]

Please could you format your post (command lines) ? It's quite unreadable for now

[ashaneev07]

Hii Thanks for the reply. I've pasted the command below.

./gatk VariantFiltration \ -R /home/Documents/Tools_NGS/VariantCall/genome_assembly.fa \  -V /media/TOSHIBAEXT/Variant_Calling/Untitled Folder/snps_300bp.vcf.gz  \ -O snp_output.vcf.gz \  --filter-expression "AB < 0.2 || MQ0 > 50" \--filter-name "my_filters"

Answer 1

[Devon Ryan]

You need an -O argument. Also, ditch all of the \ line escapes, since they're confusing your shell and making it think you specified ' -R' rather than '-R'.

[ashaneev07]

Thanks for your suggestion. I've tried with as you mensioned.But it shows the same error message.Here i've pasted my command.

 ./gatk VariantFiltration  -R /home/Documents/Tools_NGS/VariantCall/genome_assembly.fa   -V /media/TOSHIBAEXT/Variant_Calling/Untitled Folder/snps_300bp.vcf.gz  -O snp_output.vcf.gz  --filter-expression "AB < 0.2 || MQ0 > 50" --filter-name "my_filters"

[Devon Ryan]

If you're still getting the complaints about -R then try removing that option and see what happens. That could well be a GATK bug.