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Illegal division by zero error in ONCOCNV_getCounts.pl #3

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smrwf opened this issue Nov 3, 2016 · 1 comment
Open

Illegal division by zero error in ONCOCNV_getCounts.pl #3

smrwf opened this issue Nov 3, 2016 · 1 comment

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@smrwf
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smrwf commented Nov 3, 2016

I am using the wrapper shell script (ONCOCNV.sh) to run ONCOCNV (version 6.6) and am getting a division by zero error in line 462.
This issue is referred to in this thread (http://seqanswers.com/forums/showthread.php?t=50211) where it is indicated that this can be caused by a malformed bed file. I have tried using my own bed file (following the instructions for formatting) and also the file provided as part of the test dataset and get the same error in both cases.
Please could you provide some advice on how I can identify the source of this error? Many thanks.

@MarWoes
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MarWoes commented Mar 1, 2017

I had the same issue with a .bed file that has lines looking like this:

1 36931668 36931937 CSF3Rexon17line1chr13693169736932509_tile_1 0 CSF3R

Prepending chr to the chromosome column has resolved the issue for me:
chr1 36931668 36931937 CSF3Rexon17line1chr13693169736932509_tile_1 0 CSF3R

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