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DepthOfCoverage fails with java.lang.ArithmeticException: / by zero

AsmaAsma Member, Broadie

I get the following error while executing DepthOfCoverage:

Arguments: -T DepthOfCoverage -R /seq/regev_genome_portal/RESOURCES/human/Hg19/Hg19.fa -I /broad/hptmp/bankapur/RNASEQC_STAR/Aligned.sortedByCoord.out.bam.wrg.bam.resorted.bam.dups_marked.bam -o /broad/hptmp/bankapur/RNASEQC_STAR/sample/highexpr//perBaseDoC.out -L /broad/hptmp/bankapur/RNASEQC_STAR/sample/highexpr/intervals.list -l ERROR
Arguments Array: [-T, DepthOfCoverage, -R, /seq/regev_genome_portal/RESOURCES/human/Hg19/Hg19.fa, -I, /broad/hptmp/bankapur/RNASEQC_STAR/Aligned.sortedByCoord.out.bam.wrg.bam.resorted.bam.dups_marked.bam, -o, /broad/hptmp/bankapur/RNASEQC_STAR/sample/highexpr//perBaseDoC.out, -L, /broad/hptmp/bankapur/RNASEQC_STAR/sample/highexpr/intervals.list, -l, ERROR]
GATK command result code: 0
Depth of Coverage run time: 0 min
... GATK Depth of Coverage Analysis DONE
Loading transcripts
Splitting intervals into transcript-oriented DoC files
Indexing DoC result file: /broad/hptmp/bankapur/RNASEQC_STAR/sample/lowexpr//perBaseDoC.out: 0 s
Finding DoC results per transcript
DoC Results by interval have been mapped back to the transcripts: /broad/hptmp/bankapur/RNASEQC_STAR/sample/lowexpr//perBaseDoC.out: 0 s
Mapped intervals back to transcripts: 0 s
java.lang.ArithmeticException: / by zero
at org.broadinstitute.cga.rnaseq.PerBaseDoC.scale(PerBaseDoC.java:236)
at org.broadinstitute.cga.rnaseq.PerBaseDoC.calculateAverageCoverageByNormalizedPosition(PerBaseDoC.java:191)
at org.broadinstitute.cga.rnaseq.PerBaseDoC.interpretAndOutputDoCResults(PerBaseDoC.java:956)
at org.broadinstitute.cga.rnaseq.PerBaseDoC.createReports(PerBaseDoC.java:913)
at org.broadinstitute.cga.rnaseq.PerBaseDoC.createReports(PerBaseDoC.java:905)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:267)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:166)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:135)
RNA-SeQC Total Runtime: 2 min

Note, the perBaseDoC.out is empty. What do you think is going wrong here?
Thank you,
Asma

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