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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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Division by zero error in MethOverRegion? #39

Closed hyl317 closed 3 years ago

hyl317 commented 4 years ago

When plotting MethOverRegion, I got the following error message when running MethOverRegion:

Subcommand: MethOverRegion file:info.tab.txt The sample and region information is stored in file:info.tab.txt

It seemed that the reigons you provided are Genes. Please make sure of this.

Output directory is: /data/home/yh362/work/2019_Summer/epigenome/raw_reads/Root_samtools/MethOverRegion Output prefix: root A6528.root.combined.CX_report.txt.gz Nsyl Nsyl.v1.region A6528.root.combined.CX_report.txt.gz Ntom Ntom.v1.regionStart calculate methylation information for target context CG Use of uninitialized value $bin_length in division (/) at /data/home/yh362/tools/ViewBS-0.1.8/lib/Meth/OverRegion.pm line 128, line 1. Illegal division by zero at /data/home/yh362/tools/ViewBS-0.1.8/lib/Meth/OverRegion.pm line 128, line 1.

The command I have used:

~/tools/ViewBS-0.1.8/ViewBS MethOverRegion --sample file:info.tab.txt --prefix root --context CG --outdir MethOverRegion --flank 5000

However, if I don't specify --flank 5000 and just use the default values, it seems to work fine.

aer-neo commented 4 years ago

I have exactly the same problem.

xie186 commented 4 years ago

I'll look into this issue this week. Thanks.

spiya commented 4 years ago

I am also getting the same error. Do you have any suggestion?

aer-neo commented 4 years ago

Hello, I ended up using another program in order to get the "Gene Density", Batmeth2, I installed it by Anaconda3 and made it work, then I modified the R files so that the output of these graphs were in PDF instead of PNG in "BatMeth2/scripts/methylevel.elements.compare.r" and "BatMeth2/scripts/methylevel.elements.r".

El dom., 29 de marzo de 2020 21:34, Sarbo notifications@github.com escribió:

I am also getting the same error. Do you have any suggestion?

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xie186 commented 4 years ago

Sorry for the late response. I'll work on this tomorrow and let you know the results.

asumann commented 4 years ago

I have the same issue. Help needed! Thanks in advance.

xiuru commented 3 years ago

I have the same issue. Is there any suggestion?

xie186 commented 3 years ago

Please download the code using git clone https://github.com/xie186/ViewBS.git.

I'll work on other issues and release a new version. Sorry for taking such a long time to work on this.