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Help:intervals' does not match any contig in the GATK sequence dictionary derived from the reference

rcholicrcholic DenverMember

I encountered the following the error messages when I try to run the following command lines for IndelRealigner. I never saw this kind of error before with GATK. I used GATK to generate the intervals files with the same reference genome hg19.fasta. I did not change anything in hg19.fasta. Why GATK complains that this refernece is not correct? please help ...

java -Xmx8g -Djava.awt.headless=true -jar $CLASSPATH/GenomeAnalysisTK.jar \
-T IndelRealigner \
-R /Users1/GATK_ref/hg19.fasta \
-I ./bamfiles.list \
-targetIntervals ./intervals.list \
-log ../GATK/log/Realign.LOG \
-o ../GATK/AllSampleRealigned.bam
ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.7-4-g6f46d11):
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Badly formed genome loc: Contig '../GATK/F1-616R-MEM-PE.sorted.deDuped.reorder_clean_grp.intervals' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It's not complaining about the reference, it's complaining about the intervals. Apparently your interval list contains the line "../GATK/F1-616R-MEM-PE.sorted.deDuped.reorder_clean_grp.intervals", or you used a different command line than what you posted and didn't type the intervals list name correctly. In either case the problem is on your end; you need to check your files and your command line. We cannot help you with this.

  • rcholicrcholic DenverMember
    edited October 2013

    Thanks Geraldine. So you are saying I should use absolute path for the intervals files in my itervals.list file. I'll give it a try.

    edit: if I feed invidual bam and interval files, it works. I guess the IndelRealigner does not work with a list of input?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    The intervals file should contain intervals, not paths to other lists of intervals. It's not like a list of bam files, if that's what you were trying to do. This is all detailed in the input requirements documentation.

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