makeCNVcalls.R Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p :

[yusmile0618]

I have 185 female and 214 male WES samples, I successfully run female samples and no errors, but when I run 214 male samples in the makeCNVcalls.R step, Error shows : ERROR Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p :

command: $Rscript makeCNVcalls.R --Rdata male.RData --custom FALSE --out male_DECoNCalls --plot None --plotFolder DECoNPlots

end of the log file: [1] "Processing sample: PxxxF.rmdup 214/214" Optimization of the choice of aggregate reference set, this process can take some time Number of selected bins: 10000 Now fitting the beta-binomial model on a data frame with 243190 rows : this step can take a few minutes. Now computing the likelihood for the different copy number states Correlation between reference and tests count is 0.99024 To get meaningful result, this correlation should really be above 0.97. If this is not the case, consider the output of ExomeDepth as less reliable (i.e. most likely a high false positive rate) Number of calls for chromosome 1 : 64 Number of calls for chromosome 2 : 39 Number of calls for chromosome 3 : 12 Number of calls for chromosome 4 : 26 Number of calls for chromosome 5 : 27 Number of calls for chromosome 6 : 26 Number of calls for chromosome 7 : 56 Number of calls for chromosome 8 : 23 Number of calls for chromosome 9 : 25 Number of calls for chromosome 10 : 29 Number of calls for chromosome 11 : 17 Number of calls for chromosome 12 : 28 Number of calls for chromosome 13 : 2 Number of calls for chromosome 14 : 20 Number of calls for chromosome 15 : 48 Number of calls for chromosome 16 : 44 Number of calls for chromosome 17 : 23 Number of calls for chromosome 18 : 10 Number of calls for chromosome 19 : 54 Number of calls for chromosome 20 : 5 Number of calls for chromosome 21 : 8 Number of calls for chromosome 22 : 27 Number of calls for chromosome X : 23 Number of calls for chromosome Y : 3 There were 50 or more warnings (use warnings() to see the first 50) Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p : 答案矢量会太长 此外: There were 50 or more warnings (use warnings() to see the first 50) 停止执行

I don't know why, Please help me to figure out. thanks a lot!

[Charles1DENG]

i met the same error..

[bioxu]

@Charles1DENG check gene column in your bed file whether has multiple gene with comma split, this column allow only one gene.

[Charles1DENG]

Thanks for your support. The solution you provided was perfect.

I have another problem that how can i obtain the whole cnv results from DECoN results, i.e., a result with all normal exons.

Looking forward to your answer ~

发自Charles的iPhone

在 2022年8月3日，15:45，bioxu @.***> 写道：

 @Charles1DENG check gene column in your bed file whether has multiple gene with comma split, this column allow only one gene.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[doubi333]

i have fix the problem: makeCNVcall.R: [144]:gene.index=which(bed.file[,4]==genes[j]) have some problem,it will cause bed file to fail to find the correct gene name index if there are multiple names. change code: [144]:gene.index=which(grepl(genes[j],bed.file[,4])) can fix this issue.

[doubi333]

i have fix the problem: makeCNVcall.R: [144]:gene.index=which(bed.file[,4]==genes[j]) have some problem,it will cause bed file to fail to find the correct gene name index if there are multiple names. change code: [144]:gene.index=which(grepl(genes[j],bed.file[,4])) can fix this issue.

It also have some problems:makeCNVcall.R:[276]: exonRange<-which(bed.file[,4]%in%Gene) mainly because there were multiple results returning genes in the bed file or the exact position in the bed file could not be accurately found due to the comma problem. The solution was to correct the name of the bed file so that each column had only one gene name or split the bed.