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RnBeads Stuck in "STARTED Methylation Value Distributions - Sample Groups"

I am trying to run RRBS data on RnBeads, but it gets stuck at "STARTED Methylation Value Distributions - Sample Groups." I am running Bismark outputs - bismark.cov, and my sample annotation header looks like this.

Sample_ID   description filename_bismark.cov    Passage_NO  Treatment

It runs, and it creates files up to Methylation Value Distributions. First, I thought that I had too many groups, and I ran it again with BS Minimal with only 2 groups. However, it still gets stuck at the same point. I am running on 16 cores with 32 GB of RAM. I even let it ran for 4 days, but it doesn't proceed.

rnbeads rrbs
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written by magicridge • magicridge

Hello guys,

So... I tried to run it on the server, and when it got stuck on the same error message, it generated the following error message.

"a forked child should not open a graphics device"

I dug around the Internet and found out it has something to do with running on the multicore according to this post

Error: a forked child should not open a graphics device #27

So, I tried to run

> library(future.apply) 
    > plan(multisession)

plan(multisession(rnb.run.dj()))

multisession(
  Future(rnb.run.dj()),
  workers = availableCores(64),
  lazy = FALSE,
  rscript_libs = .libPaths(),
  envir = parent.frame()
)

Also, it seems it has something to do with GUI according to this post Rstudio Community.

So, I ran multisession on my computer with 16 cores and ran another one on the server. The one that I ran on my computer stalled at exactly the same process while the one that I ran on the server is still going past the previous stalling point.

If someone has the same problem as I do, try to run it on a single core. I cannot guarantee it will run, but it ran past the stalling point for me.

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written by magicridge • magicridge

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