Problem with MethCoverage (Illegal division by zero)
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This could be related to #28
So, I'm trying to follow the petit tutorial on the main page for Bismarck alignments (I've run the pipeline exactly the same as it's suggested) and with this command line /home/data/rrebollo/ViewBS-0.1.9/ViewBS MethCoverage --reference microvelia-longipes.fa --sample L1-M1-10-bmsnd.bismark.cov.gz,L1 --sample L2-M3-10-bmsnd.bismark.cov.gz,L2 --sample L3-M1-20-bmsnd.bismark.cov.gz,L3 --sample L4-M3-20-bmsnd.bismark.cov.gz,L4 --outdir methCoverage --prefix microvelia-longipes
I'm getting the following error:
Subcommand: MethCoverage
Sample(s): L1-M1-10-bmsnd.bismark.cov.gz,L1 L2-M3-10-bmsnd.bismark.cov.gz,L2 L3-M1-20-bmsnd.bismark.cov.gz,L3 L4-M3-20-bmsnd.bismark.cov.gz,L4
Output directory is: /home/data/rrebollo/mlongipes/LuisAF/12-02-2020/methCoverage
Output prefix: microvelia-longipes
Start reading the methylation file
Even cytosine sites with 0 read covered was outputted so we are going to use the total row numbers for CG (CHG/CHH) as Denominator
Use of uninitialized value in multiplication (*) at /home/data/rrebollo/ViewBS-0.1.9/lib/Meth/Coverage.pm line 114.
Illegal division by zero at /home/data/rrebollo/ViewBS-0.1.9/lib/Meth/Coverage.pm line 114.
Is this caused by extremely low coverage, is there any recommendation for this error?
Cheers,
Luis Alfonso.
Hi Luis Alfonso,
Thanks for using ViewBS. Are you using the latest version? If so, would you be able to send me a piece of the file you are using? Thanks. My email is xie186@purdue.edu
Best,
Shaojun
Hey Shaojun,
I just sent it through we transfer the files I'm using,
Cheers,
Luis Alfonso.
I'll take a look and get back to you (probably tomorrow). Thanks.
Sorry for the late response. Kids were sick. I didn't see the reference genome. You can either send it to me or tell me the link to download. Thanks.
Hey, don't worry, kids first, I just shared the genome file through drive.
Hey Shaojun, did you had time to check the data?