QC3 VCF Error

[boxiangliu]

Hello,

I am running QC3 on a VCF file with 1 sample, I am using the following command
perl /srv/persistent/bliu2/tools/QC3/qc3.pl -m v -i $inputFile -o $outputDir

And I am getting the following error:
Error in FUN(X[[i]], ...) :
only defined on a data frame with all numeric variables
Calls: showConsistence ... col_by_value -> seq -> Summary.data.frame -> lapply -> FUN
Execution halted

It seems like this error originates from a piece of R code. However, I could not pin down where the error originates exactly. Could you provide some guidance on debugging? Any information will be highly appreciated!

[slzhao]

Hi Boxiang, I think it is related to the format of vcf file. Would you please run the example vcf file first? If it works, then would you please send me some lines of your vcf file? So that I can check which part makes the error message. Thanks! Shilin 2016-11-21 15:00 GMT-06:00 Boxiang Liu <notifications@github.com>:

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Hello, I am running QC3 on a VCF file with 1 sample, I am using the following command perl /srv/persistent/bliu2/tools/QC3/qc3.pl -m v -i $inputFile -o $outputDir And I am getting the following error: Error in FUN(X[[i]], ...) : only defined on a data frame with all numeric variables Calls: showConsistence ... col_by_value -> seq -> Summary.data.frame -> lapply -> FUN Execution halted It seems like this error originates from a piece of R code. However, I could not pin down where the error originates exactly. Could you provide some guidance on debugging? Any information will be highly appreciated! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABmyjf8Oks0FQsKjPt28ONnbGDzkBQMmks5rAgZtgaJpZM4K4sOX> .