Error in ExomeCNV running

[croshong]

Hi all

I want to use ExomeCNV to call CNV from my NGS result


But when I try I got this kind of error

> library(ExomeCNV)
Loading required package: DNAcopy
> chr.list=paste("chr",c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y"),sep="")
> normal_set1 = read.coverage.gatk("test_res1/set1_d/coverage/1532SD.REF_Y.sample_interval_summary")
> tumor_set1 = read.coverage.gatk("test_res1/set1_d/coverage/1768.REF_Y.sample_interval_summary")
> logR_set1 = calculate.logR(normal_set1,tumor_set1)
> eCNV_set1 = c()
> for (i in 1:length(chr.list)) {
+ idx = (normal_set1$chr = chr.list[i])
+ ecnv = classify.eCNV(normal=normal_set1[idx,], tumor=tumor_set1[idx,], logR=logR_set1[idx], min.spec=0.9999, min.sens=0.9999, option="spec", c=0.5, l=70)
+ eCNV_set1 = rbind(eCNV_set1,ecnv)
+ }
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
[1] "analyzing eCNV with min.spec 0.9999 and min.sens 0.9999 and option to maximize spec"
> cnv_set1 = multi.CNV.analyze(normal_set1, tumor_set1, logR=logR_set1, all.cnv.ls=list(eCNV_set1), coverage.cutoff=5, min.spec=0.99, min.sens=0.99, option="auc", c=0.5)
Error in sort(abs(diff(genomdat)))[1:n.keep] :
only 0's may be mixed with negative subscripts
Calls: multi.CNV.analyze -> CNV.analyze -> smooth.CNA -> trimmed.variance
In addition: Warning message:
In CNA(norm.log.ratio[well.covered.exon.idx], strip.chr.name(normal$chr[well.covered.exon.idx]), :
markers with missing chrom and/or maploc removed

Execution halted

The example data in tutorial works well

So, It seems that my data has a problem, But I couldn't find what's wrong

Any kind of advice would be welcome

Thanks