" 'end' must be >= 'start' - 1" error in cn.mops
1
0
Entering edit mode
User000 • 0
@ea03770f
Last seen 24 months 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 • 898 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day 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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 756 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6