Error Message - ZeroDivisionError: integer division or modulo by zero

[etvedte]

Greetings,

I'm trying to use ploidyNGS to make predictions about putatively haploid/diploid datasets. I followed the documentation and received the following error:

./ploidyNGS.py --guess_ploidy -o DF_genome -d 100000 -b DF_I_DNA_genome_SORTED.bam ###############################################################

This is ploidyNGS version v3.1.2

Current date and time: Thu Feb 22 16:20:01 2018

############################################################### BAM index present... OK! Number of mapped reads from BAM: 31817941 Traceback (most recent call last): File "./ploidyNGS.py", line 130, in averageCoverage=countTotalReads/countTotalPositions ZeroDivisionError: integer division or modulo by zero

I'm guessing by the error output that the denominator in averageCoverage is zero, but that shouldn't be the case. My bam file contains a large eukaryotic genome with lots of scaffolds, but I wanted to test using the -d flag as a first pass before splitting bam into scaffolds. Any help is appreciated!

[diriano]

you may have scaffold with very low coverage, and these are giving rise to the problem. I would suggest to run ploidyNGS on well covered scaffolds, at least 50x.

[aldembert]

Ok thanks a lot Diego!

On Thu, Jan 31, 2019 at 9:39 AM Diego Mauricio Riaño-Pachón < notifications@github.com> wrote:

you may have scaffold with very low coverage, and these are giving rise to the problem. I would suggest to run ploidyNGS on well covered scaffolds, at least 50x.

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