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
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.
