ZeroDivisionError: float division by zero when computingGC.

[shathaa92]

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]

Hi,

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

Thanks,
Ana

[zstephens]

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