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

wubinwubin ChinaMember

Dear Geraldine,
I encountered the following the error messages when I try to run the following command lines for SomaticIndelDetector(GATK,v2.1-8-g5efb575),which I had been successful in before. the ./chrall is the interval file which contains intervals where Indels located in these areas are supposed to be detected by gatk and are generated by the fasta file of hg19. what's with the command line? the fasta file, or the interval file?

java -Xmx8g -jar ./GenomeAnalysisTK.jar \
-l INFO \
-R ./ucsc.hg19.fasta \
-T SomaticIndelDetector \
--unpaired -I ./output.recal.cleaned.bam \
-bed ./output.indel.bed \
-o ./output.indel.vcf \
-L ./chrall

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.1-8-g5efb575):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: Badly formed genome loc: Contig './chrall' does not match any contig in the GATK sequen

ce dictionary derived from the reference; are you sure you are using the correct reference fasta file?

ERROR ------------------------------------------------------------------------------------------


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