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ZeroDivisionError: float division by zero when computingGC. #49

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shathaa92 opened this issue Aug 30, 2018 · 2 comments
Open

ZeroDivisionError: float division by zero when computingGC. #49

shathaa92 opened this issue Aug 30, 2018 · 2 comments

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@shathaa92
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Dear Zach,
I trying to computeGC.py and I have generated a genomecov file from bedtools as fellow:
bedtools genomecov -d -ibam id.sorted.bam -g ${ref} > id.genomecov
then I took id.genomecov to computeGC by neat:
python ${neat}utilities/computeGC.py -r ${ref} -i id.genomecov -w 50000 -o id_GC_models.p
I got this result:
line 103, in
avgCov = allMean/float(runningTot)
ZeroDivisionError: float division by zer

Any suggestions on how I can fix it or maybe change the sliding window? Any help is appreciated !
Thank you in advance.

Regards
Shatha

@popicka
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popicka commented Nov 22, 2020

Hi,

I got the same error. Is there any advice on how this could be avoided?

Thanks,
Ana

@zstephens
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zstephens commented Nov 23, 2020

Do the contig names in the genomecov file match the contig names in the reference fasta exactly?

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