Error in dba.count and dba.analyze
1
0
Entering edit mode
Mar Mar ▴ 20
@mar-mar-23198
Last seen 19 months ago

Hello All,

I have 300 chIP peaksets. I am trying to count and analyze them using DiffBind. However when I am running the code, I get the following error. Will appreciate any suggestion to fix it. Many thanks.

dba.count ... dba.parallel.lapply -> <anonymous> -> mclapply -> lapply -> FUN -> mcfork Execution halted Error while shutting down parallel: unable to terminate some child processes

DiffBind chip-seq differentially-binding-site • 453 views
1
Entering edit mode
Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 4 days ago
CRUK, Cambridge, UK

This is a fairly generic error that something unspecified went wrong in one or more of the parallel threads.

You can try running dba,count()with bParallel=FALSE to see what the errors are. If the messages are not clear, you can report back here and I may be bale to help.

One thing I have seen happen with a large number of peaksets (300) is that, if by default your machine allocates a large number of cores to parallel tasks, there may not be enough memory to deal. This is easily dealt with by manually setting the number of cores as a $config$cores option.