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Variant Discovery in High-Throughput Sequencing Data

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GenomicsDBImport genomicsdb-workspace-path not recognized

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  • Avatar
    Genevieve Brandt (she/her)

    Hi Lance Heady, could you send your entire error log?

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  • Avatar
    Lance Heady

    Sorry about that Genevieve Brandt (she/her), here you go (this is from the script where I had all of my ~180 files as inputs): 

     

    using /tmp/launcher.1793505.hostlist.DcvcMTRx to get hosts
    starting job on Nucleus094
    Using GATK jar /project/psychiatry/Madabhushi_lab/s430286/gatk-4.1.2.0/gatk-package-4.1.2.0-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 /project/psychiatry/Madabhushi_lab/s430286/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar GenomicsDBImport
    USAGE: GenomicsDBImport [arguments]

    Import VCFs to GenomicsDB
    Version:4.1.2.0


    Required Arguments:

    --genomicsdb-workspace-path:String
    Workspace for GenomicsDB. Must be a POSIX file system path, but can be a relative path.
    Must be an empty or non-existent directory. Required.

    --intervals,-L:String One or more genomic intervals over which to operate This argument must be specified at
    least once. 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.

    --batch-size:Integer Batch size controls the number of samples for which readers are open at once and therefore
    provides a way to minimize memory consumption. However, it can take longer to complete.
    Use the consolidate flag if more than a hundred batches were used. This will improve
    feature read time. batchSize=0 means no batching (i.e. readers for all samples will be
    opened at once) Defaults to 0 Default value: 0.

    --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: 0.

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

    --consolidate,-consolidate:Boolean
    Boolean flag to enable consolidation. If importing data in batches, a new fragment is
    created for each batch. In case thousands of fragments are created, GenomicsDB feature
    readers will try to open ~20x as many files. Also, internally GenomicsDB would consume
    more memory to maintain bookkeeping data from all fragments. Use this flag to merge all
    fragments into one. Merging can potentially improve read performance, however overall
    benefit might not be noticeable as the top Java layers have significantly higher
    overheads. This flag has no effect if only one batch is used. Defaults to false Default
    value: false. Possible values: {true, false}

    --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}

    --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: .

    --genomicsdb-segment-size:LongBuffer size in bytes allocated for GenomicsDB attributes during import. Should be large
    enough to hold data from one site. Defaults to 1048576 Default value: 1048576.

    --genomicsdb-vcf-buffer-size,-genomicsdb-vcf-buffer-size:Long
    Buffer size in bytes to store variant contexts. Larger values are better as smaller values
    cause frequent disk writes. Defaults to 16384 which was empirically determined to work
    well for many inputs. Default value: 16384.

    --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}

    --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}

    --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. Improves performance using large
    lists of intervals, as in exome sequencing, especially if GVCF data only exists for
    specified intervals. Default value: false. Possible values: {true, false}

    --overwrite-existing-genomicsdb-workspace:Boolean
    Will overwrite given workspace if it exists. Otherwise a new workspace is created.
    Defaults to false Default value: false. Possible values: {true, false}

    --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,
    MateOnSameContigOrNoMappedMateReadFilter, MateUnmappedAndUnmappedReadFilter,
    MetricsReadFilter, NonChimericOriginalAlignmentReadFilter,
    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.

    --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}

    --validate-sample-name-map,-validate-sample-name-map:Boolean
    Boolean flag to enable checks on the sampleNameMap file. If true, tool checks
    whetherfeature readers are valid and shows a warning if sample names do not match with the
    headers. Defaults to false Default value: false. Possible values: {true, false}

    --variant,-V:String GVCF files to be imported to GenomicsDB. Each file must containdata for only a single
    sample. Either this or sample-name-map must be specified. This argument may be specified
    0 or more times. Default value: null. Cannot be used in conjuction with argument(s)
    sampleNameMapFile

    --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}

    --max-num-intervals-to-import-in-parallel,-max-num-intervals-to-import-in-parallel:Integer
    Max number of intervals to import in parallel; higher values may improve performance, but
    require more memory and a higher number of file descriptors open at the same time Default
    value: 1.

    --reader-threads,-reader-threads:Integer
    How many simultaneous threads to use when opening VCFs in batches; higher values may
    improve performance when network latency is an issue. Multiple reader threads are not
    supported when running with multiple intervals. Default value: 1.

    --sample-name-map:String Path to file containing a mapping of sample name to file uri in tab delimited format. If
    this is specified then the header from the first sample will be treated as the merged
    header rather than merging the headers, and the sample names will be taken from this file.
    This may be used to rename input samples. This is a performance optimization that relaxes
    the normal checks for consistent headers. Using vcfs with incompatible headers may result
    in silent data corruption. Default value: null. Cannot be used in conjuction with
    argument(s) variantPaths (V)

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


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

    A USER ERROR has occurred: Argument genomicsdb-workspace-path was missing: Argument 'genomicsdb-workspace-path' is required.

    ***********************************************************************
    Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
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    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: --: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: --: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]
    /home2/s430286/bin/launcher//launcher: line 105: eval: -L: invalid option
    eval: usage: eval [arg ...]

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  • Avatar
    Genevieve Brandt (she/her)

    It looks like none of your arguments are getting accepted. 

    This line would appear with all your arguments if the command was using them: "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 /project/psychiatry/Madabhushi_lab/s430286/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar GenomicsDBImport
    USAGE: GenomicsDBImport [arguments]"

    Also, later in your error message, your arguments are being evaluated with bash, not GATK "/home2/s430286/bin/launcher//launcher: line 105: eval: -V: invalid option
    eval: usage: eval [arg ...]"

    Something seems to be wrong with the way you are submitting your command line. I would recommend trying to submit the command on one line first, and also try other ways of writing it so you are not making errors without realizing. From what you have written, it does not seem wrong, but there is an issue since none of the input arguments are being recognized. 

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