CountTerminusEvent and Output

jreutherjreuther Posts: 3Member

Hi, 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? Jacquelyn

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,809Administrator, GATK Developer 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.

    image

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

    Screen Shot 2013-11-05 at 5.22.02 PM.png
    726 x 49 - 10K

    Geraldine Van der Auwera, PhD

  • jreutherjreuther Posts: 3Member

    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. Jacquelyn

    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 file -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 -home-and-how-does-it-affect-me#latest for details. (NO_ET|STANDARD|AWS| STDOUT) -K,--gatk_key GATK Key file. Required if running with -et NO_ET. Please see -home-and-how-does-it-affect-me#latest 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 file) -isr,--interval_set_rule Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs (UNION| INTERSECTION) -im,--interval_merging Indicates the interval merging rule we should use for abutting intervals (ALL| OVERLAPPING_ONLY) -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 generator. -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 (NANOSECONDS|MICROSECONDS|MILLISECONDS| SECONDS|MINUTES|HOURS|DAYS) -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 here (NONE|ALL_READS|BY_SAMPLE) -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 the engine (OFF|CALCULATE_AS_NECESSARY| RECALCULATE) -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 recalibration -DIQ,--disable_indel_quals If true, disables printing of base insertion and base deletion tags (with -BQSR) -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. (ALLOW_UNINDEXED_BAM| ALLOW_UNSET_BAM_SORT_ORDER| NO_READ_ORDER_VERIFICATION| ALLOW_SEQ_DICT_INCOMPATIBILITY| LENIENT_VCF_PROCESSING|ALL) -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 monitoring -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 line. -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| SILENT) -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: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_qc_CountTerminusEvent.html

    cgm-555871:~ jacquelyn$

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