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DepthofCoverage, argument with name 'includeRefNSites' isn't defined?


I am trying to run a depth of coverage calculation as part of the XHMM workflow for cnv analysis. Upon running the following bash code, I am returned with this error.

java -Xmx3072m -jar ./Sting/dist/GenomeAnalysisTK.jar \
-T DepthOfCoverage -I group1.READS.bam.list -L EXOME.interval_list \
-R ./human_g1k_v37.fasta \
-dt BY_SAMPLE -dcov 5000 -l INFO --omitDepthOutputAtEachBase --omitLocusTable \
--minBaseQuality 0 --minMappingQuality 20 --start 1 --stop 5000 --nBins 200 \
--includeRefNSites \
-o group1.DATA

ERROR MESSAGE: Argument with name 'includeRefNSites' isn't defined.



Best Answers


  • Yes, thank you!

    But now it seems that I am running into another problem. I created an interval_list file, and tested the first few lines of coordinates, which worked fine. However, upon trying it with all of the coordinates, I received the following error:

    ERROR MESSAGE: File associated with name /scratch/stevenlovesscience/CLP/xhmm_ref/final_intervals.interval_list is malformed: Interval file could not be parsed in any supported format. caused by Failed to parse Genome Location string: 1:-91812866

    My interval_list looks like this:

    Any insight would be greatly appreciated!

  • Alright, one last question (hopefully), after fixing my intervals this was the output given in my command line, is this how it should appear for depth of coverage calculation? :
    T_FRAGMENTS -o /scratch/stevenlovesscience/CLP/RPKM/
    INFO 12:56:43,204 HelpFormatter - Executing as [email protected] on Linux 2.6.32-220.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_71-b14.
    INFO 12:56:43,204 HelpFormatter - Date/Time: 2014/11/08 12:56:43
    INFO 12:56:43,204 HelpFormatter - ---------------------------------------------------------------------------------------------
    INFO 12:56:43,205 HelpFormatter - ---------------------------------------------------------------------------------------------
    INFO 12:56:43,649 GenomeAnalysisEngine - Strictness is SILENT
    INFO 12:56:43,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 5000
    INFO 12:56:43,725 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 12:56:43,789 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
    INFO 12:56:44,119 IntervalUtils - Processing 33356897 bp from intervals
    INFO 12:56:44,180 GenomeAnalysisEngine - Preparing for traversal over 3 BAM files
    INFO 12:56:44,646 GenomeAnalysisEngine - Done preparing for traversal
    INFO 12:56:44,646 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
    INFO 12:56:44,646 DepthOfCoverage - Per-Locus Depth of Coverage output was omitted
    INFO 12:57:14,650 ProgressMeter - 1:11775175 1.21e+06 30.0 s 24.0 s 0.7% 68.4 m 67.9 m
    INFO 12:57:44,652 ProgressMeter - 1:23235514 2.25e+06 60.0 s 26.0 s 1.5% 68.6 m 67.6 m
    INFO 12:58:14,653 ProgressMeter - 1:33612977 3.15e+06 90.0 s 28.0 s 2.1% 70.6 m 69.1 m
    INFO 12:58:44,655 ProgressMeter - 1:43647404 3.91e+06 120.0 s 30.0 s 2.8% 72.4 m 70.4 m
    INFO 12:59:14,657 ProgressMeter - 1:55161048 4.96e+06 2.5 m 30.0 s 3.4% 73.7 m 71.2 m
    INFO 12:59:44,658 ProgressMeter - 1:85117665 5.50e+06 3.0 m 32.0 s 4.0% 74.9 m 71.9 m
    INFO 13:00:14,658 ProgressMeter - 1:109566076 6.09e+06 3.5 m 34.0 s 4.6% 75.7 m 72.2 m
    INFO 13:00:44,659 ProgressMeter - 1:120512233 6.83e+06 4.0 m 35.0 s 5.2% 76.7 m 72.7 m ...

    Once again, thank you very much indeed for your time.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Steven,

    That's the expected log output, yes. The actual results will be in the output files.

  • Brilliant! Thank you very much indeed Geraldine! I commend your dedication to your users, the Broad is lucky to have you.

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