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How do I filter the reads that result in this type of error in some of my intervals?

severinseverin Member
edited December 2012 in Ask the GATK team
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Only one of refStart or refStop must be < 0, not both (-1, -8)

Here is some information

INFO  20:22:19,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-16-g9f648cb, Compiled 2012/12/04 03:48:10 
INFO  20:22:19,452 HelpFormatter - Program Args: -T HaplotypeCaller


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Severin, can you please post the entire stack trace including your commandline?

  • severinseverin Member
    edited December 2012

    Here is everything I have from the output and Error file.
    I know it occurs in the first interval of the first chromosome.

    Here is my command
    java -Xmx3072m -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -cp /data004/software/GIF/GIF/programs/Queue-2.2-16-g9f648cb/Queue.jar org.broadinstitute.sting.gatk.CommandLineGATK -T HaplotypeCaller -I /data006/GIF_2/Client/GATK-64/$3.realign.bam -L /data006/GIF_2/Client/GATK-64/.queue/scatterGather/script-1-sg/temp_01_of_64/scatter.intervals -R /data006/GIF_2/Client/GATK-64/Species.fasta -o /data006/GIF_2/Client/GATK-64/.queue/scatterGather/script-1-sg/temp_01_of_64/$3.realign.queue.vcf -stand_emit_conf 10.0

    In case you are wondering I couldn't get Queue to finish but it did create the split commands and the intervals and output the commands it was trying to run. 63/64 of those commands ran without a problem this one I believe is complaining about some of the reads in the BAM file but I don't know which as I don't understand the error. I saw there was another post on this but its resolution was not clear.

    ERROR stack trace

    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Only one of refStart or refStop must be < 0, not both (-1, -8)
    at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinates(
    at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipByReferenceCoordinatesLeftTail(
    at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipToRegion(
    at org.broadinstitute.sting.utils.clipping.ReadClipper.hardClipToRegion(
    at org.broadinstitute.sting.utils.activeregion.ActiveRegion.hardClipToActiveRegion(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(
    at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.traverse(
    at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
    at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.commandline.CommandLineProgram.start(
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.2-16-g9f648cb):
    ERROR Please visit the wiki to see if this is a known problem
    ERROR If not, please post the error, with stack trace, to the GATK forum
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions
    ERROR MESSAGE: Only one of refStart or refStop must be < 0, not both (-1, -8)
    ERROR ------------------------------------------------------------------------------------------

    Warning: no access to tty (Bad file descriptor).
    Thus no job control in this shell.
    INFO 20:24:17,417 HelpFormatter - ---------------------------------------------------------------------------------
    INFO 20:24:17,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-16-g9f648cb, Compiled 2012/12/04 03:48:10
    INFO 20:24:17,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 20:24:17,420 HelpFormatter - For support and documentation go to
    INFO 20:24:17,425 HelpFormatter - Program Args: -T HaplotypeCaller -I /data006/GIF_2/Client/GATK-64/lane3alluniq.realign.bam -L /data006/GIF_2/Client/GATK-64/.queue/
    scatterGather/script-1-sg/temp_01_of_64/scatter.intervals -R /data006/GIF_2/Client/GATK-64/Species.fasta -o /data006/GIF_2/Client/GATK-64/.queue/scatterGather/script-1-s
    g/temp_01_of_64/lane3alluniq.realign.queue.vcf -stand_emit_conf 10.0
    INFO 20:24:17,425 HelpFormatter - Date/Time: 2012/12/14 20:24:17
    INFO 20:24:17,425 HelpFormatter - ---------------------------------------------------------------------------------
    INFO 20:24:17,425 HelpFormatter - ---------------------------------------------------------------------------------
    INFO 20:24:17,462 GenomeAnalysisEngine - Strictness is SILENT
    INFO 20:24:17,903 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE Target Coverage: 1000
    INFO 20:24:17,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
    INFO 20:24:17,978 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
    INFO 20:24:18,149 GenomeAnalysisEngine - Processing 15208505 bp from intervals
    INFO 20:24:18,159 ProgressMeter - Location regions runtime regions completed total.runtime remaining
    INFO 20:24:32,692 GATKRunReport - Uploaded run statistics report to AWS S3

  • I have done some follow up and can reproduce the error with -L Chr1:1-1000
    but not -L Chr1:2-1000 or any other interval between 2 and 1000 such as Chr 1-100, 900-1000 and others. Is it possible that this has something to do with the Haplotype caller or assembly during the Haplotypecaller?

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