Entering edit mode
2.5 years ago
magicridge
•
0
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.
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
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.