" 'end' must be >= 'start' - 1" error in cn.mops
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User000 • 0
@ea03770f
Last seen 28 days ago
Italy

I have some difficulty debugging the error cn.mops gives me below. I checked my bed file does not have start values larger than end abd neither in my gr file there are any negative values. Any idea how to solve this?

> resCNMOPS <- exomecn.mops(bamDataRanges)
Normalizing...
Starting local modeling, please be patient...  
Reference sequence:  chr1
Reference sequence:  chr2
Reference sequence:  chr3
Reference sequence:  chr4
Reference sequence:  chr5
Reference sequence:  chr6
Reference sequence:  chr7
Reference sequence:  chr8
Reference sequence:  chr9
Reference sequence:  chr10
Reference sequence:  chr11
Reference sequence:  chr12
Reference sequence:  chr13
Reference sequence:  chr14
Reference sequence:  chr15
Reference sequence:  chr16
Reference sequence:  chr17
Reference sequence:  chr18
Reference sequence:  chr19
Reference sequence:  chr20
Reference sequence:  chr21
Reference sequence:  chr22
Reference sequence:  chrX
Reference sequence:  chrY
Starting segmentation algorithm...
Using "fastseg" for segmentation.
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  In range 21: 'end' must be >= 'start' - 1.
cn.mops • 239 views
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@james-w-macdonald-5106
Last seen 31 minutes ago
United States

You can try either running exomecn.mops under the debugger, or you might get a reasonable clue by using traceback() right after the error, or alternatively by setting options(error = "recover") prior to running the function. But unless you can provide some self-contained code that reproduces the error, it's probably up to you to debug.

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Entering edit mode

Thanks for your comment. I solved the problem. Apparently the bed file was not sorted. After I sorted it works perfectly.

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