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CountTerminusEvent and Output

I was trying to use the CountTerminusEvent walker and put the following in my bash:

java -Xmx4g -jar /Users/jacquelyn/GenomeAnalysisTK.jar -R /Users/jacquelyn/Sequencing/chr1.fa -T CountTerminusEvent -I /Users/jacquelyn/Desktop/10.NA12878/R_2013_06_24_09_51_35_user_NCR-42-Killary10NA12878r_Auto_user_NCR-42-Killary10NA12878r_43.bam -L /Users/jacquelyn/DeepSeqData/IAD33712_Designed.bed -o /Users/jacquelyn/Desktop/10.NA12878TerminusEvent.txt

I kept getting the error that the argument "o" was not defined. When I queried "CountTerminusEvent -h" in my bash to get help, "--out" wasn't even listed as an argument. I feel stupid asking this question, but what am I doing wrong?

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    I checked and -o/--out is listed, both in the tech doc and in the console output (see screenshot). You may have missed it because it's all the way after the engine arguments.


    Any chance you have two spaces instead of one before after the -o in your command line?

  • jreutherjreuther Member

    That was the first thing I checked when I got the error. I went back in my console output and re-searched for the -o (even pasted it into TextEdit and did a Find command there). I hate to paste it all but I feel that is the only way you can see exactly what I am seeing (see below). I have never had this issue before. I even used the previous command I did that worked and just changed the walker, leaving the output as the same from the previous entry that worked and it didn't work this time, giving me the same error that the "o" argument isn't defined. I am at a loss for what to do. The documentation on the website clearly states that -o is an argument, and its always clearly worked for me, but when i look at the arguments on the version I am running, -o isn't an option. Sorry for the trouble.

    cgm-555871:~ jacquelyn$ java -Xmx4g -jar /Users/jacquelyn/GenomeAnalysisTK.jar -T CountTerminusEvent -h

    The Genome Analysis Toolkit (GATK) v2.4-3-g2a7af43, Compiled 2013/02/27 12:18:19
    Copyright (c) 2010 The Broad Institute

    For support and documentation go to http://www.broadinstitute.org/gatk

    usage: java -jar GenomeAnalysisTK.jar -T [-args ] [-I ] [-rbs ] [-et
    ] [-K ] [-tag ] [-rf ] [-L ] [-XL ] [-isr
    ] [-im ] [-ip ] [-R ] [-ndrs]
    [--disableRandomization] [-maxRuntime ] [-maxRuntimeUnits ] [-dt ]
    [-dfrac ] [-dcov ] [-baq ] [-baqGOP ]
    [-fixMisencodedQuals] [-allowPotentiallyMisencodedQuals] [-PF ] [-OQ] [-BQSR ] [-DIQ] [-EOQ]
    [-preserveQ ] [-globalQScorePrior ] [-allowBqsrOnReducedBams] [-DBQ
    ] [-S ] [-rpr] [-kpr] [-U ] [-nt ] [-nct
    ] [-mte] [-bfh ] [-rgbl ] [-ped
    ] [-pedString ] [-pedValidationType ] [-l ] [-log
    ] [-h] [-version] [-filterMBQ]

    -T,--analysis_type Type of analysis to run
    -args,--arg_file Reads arguments from the specified
    -I,--input_file SAM or BAM file(s)
    -rbs,--read_buffer_size Number of reads per SAM file to buffer
    in memory
    -et,--phone_home What kind of GATK run report should we
    generate? STANDARD is the default, can
    be NO_ET so nothing is posted to the
    run repository. Please see
    for details. (NO_ET|STANDARD|AWS|
    -K,--gatk_key GATK Key file. Required if running
    with -et NO_ET. Please see
    for details.
    -tag,--tag Arbitrary tag string to identify this
    GATK run as part of a group of runs,
    for later analysis
    -rf,--read_filter Specify filtration criteria to apply
    to each read individually
    -L,--intervals One or more genomic intervals over
    which to operate. Can be explicitly
    specified on the command line or in a
    file (including a rod file)
    -XL,--excludeIntervals One or more genomic intervals to
    exclude from processing. Can be
    explicitly specified on the command
    line or in a file (including a rod
    -isr,--interval_set_rule Indicates the set merging approach the
    interval parser should use to combine
    the various -L or -XL inputs (UNION|
    -im,--interval_merging Indicates the interval merging rule we
    should use for abutting intervals (ALL|
    -ip,--interval_padding Indicates how many basepairs of
    padding to include around each of the
    intervals specified with the
    -L/--intervals argument
    -R,--reference_sequence Reference sequence file
    -ndrs,--nonDeterministicRandomSeed Makes the GATK behave non
    deterministically, that is, the random
    numbers generated will be different in
    every run
    --disableRandomization Completely eliminates randomization
    from nondeterministic methods. To be
    used mostly in the testing framework
    where dynamic parallelism can result
    in differing numbers of calls to the
    -maxRuntime,--maxRuntime If provided, that GATK will stop
    execution cleanly as soon after
    maxRuntime has been exceeded,
    truncating the run but not exiting
    with a failure. By default the value
    is interpreted in minutes, but this
    can be changed by maxRuntimeUnits
    -maxRuntimeUnits,--maxRuntimeUnits The TimeUnit for maxRuntime
    -dt,--downsampling_type Type of reads downsampling to employ
    at a given locus. Reads will be
    selected randomly to be removed from
    the pile based on the method described
    -dfrac,--downsample_to_fraction Fraction [0.0-1.0] of reads to
    downsample to
    -dcov,--downsample_to_coverage Coverage [integer] to downsample to at
    any given locus; note that downsampled
    reads are randomly selected from all
    possible reads at a locus. For
    non-locus-based traversals (eg.,
    ReadWalkers), this sets the maximum
    number of reads at each alignment
    start position.
    -baq,--baq Type of BAQ calculation to apply in
    -baqGOP,--baqGapOpenPenalty BAQ gap open penalty (Phred Scaled).
    Default value is 40. 30 is perhaps
    better for whole genome call sets
    -fixMisencodedQuals,--fix_misencoded_quality_scores Fix mis-encoded base quality scores
    -allowPotentiallyMisencodedQuals,--allow_potentially_misencoded_quality_scores Do not fail when encountering base
    qualities that are too high and that
    seemingly indicate a problem with the
    base quality encoding of the BAM file
    -PF,--performanceLog If provided, a GATK runtime
    performance log will be written to
    this file
    -OQ,--useOriginalQualities If set, use the original base quality
    scores from the OQ tag when present
    instead of the standard scores
    -BQSR,--BQSR The input covariates table file which
    enables on-the-fly base quality score
    -DIQ,--disable_indel_quals If true, disables printing of base
    insertion and base deletion tags (with
    -EOQ,--emit_original_quals If true, enables printing of the OQ
    tag with the original base qualities
    (with -BQSR)
    -preserveQ,--preserve_qscores_less_than Bases with quality scores less than
    this threshold won't be recalibrated
    (with -BQSR)
    -globalQScorePrior,--globalQScorePrior The global Qscore Bayesian prior to
    use in the BQSR. If specified, this
    value will be used as the prior for
    all mismatch quality scores instead of
    the actual reported quality score
    -allowBqsrOnReducedBams,--allow_bqsr_on_reduced_bams_despite_repeated_warnings Do not fail when running base quality
    score recalibration on a reduced BAM
    file even though we highly recommend
    against it
    -DBQ,--defaultBaseQualities If reads are missing some or all base
    quality scores, this value will be
    used for all base quality scores
    -S,--validation_strictness How strict should we be with
    validation (STRICT|LENIENT|SILENT)
    -rpr,--remove_program_records Should we override the Walker's
    default and remove program records
    from the SAM header
    -kpr,--keep_program_records Should we override the Walker's
    default and keep program records from
    the SAM header
    -U,--unsafe If set, enables unsafe operations:
    nothing will be checked at runtime.
    For expert users only who know what
    they are doing. We do not support
    usage of this argument.
    -nt,--num_threads How many data threads should be
    allocated to running this analysis.
    -nct,--num_cpu_threads_per_data_thread How many CPU threads should be
    allocated per data thread to running
    this analysis?
    -mte,--monitorThreadEfficiency Enable GATK threading efficiency
    -bfh,--num_bam_file_handles The total number of BAM file handles
    to keep open simultaneously
    -rgbl,--read_group_black_list Filters out read groups matching
    : or a .txt file
    containing the filter strings one per
    -ped,--pedigree Pedigree files for samples
    -pedString,--pedigreeString Pedigree string for samples
    -pedValidationType,--pedigreeValidationType How strict should we be in validating
    the pedigree information? (STRICT|
    -l,--logging_level Set the minimum level of logging, i.e.
    setting INFO get's you INFO up to
    FATAL, setting ERROR gets you ERROR
    and FATAL level logging.
    -log,--log_to_file Set the logging location
    -h,--help Generate this help message
    -version,--version Output version information

    Arguments for MalformedReadFilter:
    -filterMBQ,--filter_mismatching_base_and_quals if a read has mismatching number of bases and base qualities, filter
    out the read instead of blowing up.

    Available Reference Ordered Data types:
    Name FeatureType Documentation
    BCF2 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_bcf2_BCF2Codec.html
    BEAGLE BeagleFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_beagle_BeagleCodec.html
    BED BEDFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_bed_BEDCodec.html
    BEDTABLE TableFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_table_BedTableCodec.html
    EXAMPLEBINARY Feature http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_example_ExampleBinaryCodec.html
    GELITEXT GeliTextFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_gelitext_GeliTextCodec.html
    OLDDBSNP OldDbSNPFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broad_tribble_dbsnp_OldDbSNPCodec.html
    RAWHAPMAP RawHapMapFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_hapmap_RawHapMapCodec.html
    REFSEQ RefSeqFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html
    SAMPILEUP SAMPileupFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_sampileup_SAMPileupCodec.html
    SAMREAD SAMReadFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_samread_SAMReadCodec.html
    TABLE TableFeature http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_table_TableCodec.html
    VCF VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_vcf_VCFCodec.html
    VCF3 VariantContext http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_vcf_VCF3Codec.html

    For a full description of this walker, see its GATKdocs at:

    cgm-555871:~ jacquelyn$

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