Question: DiffBind count warning
gravatar for ghosos
21 months ago by
ghosos0 wrote:

Hello, I am trying to calculate the FRiP score through dba.count() method as following, and I've been continuously getting this warning:

> compareCount <- dba.count(compare, bParallel=FALSE)

Sample: trimmed_DKO_R1.fastq.gz.sam.sort.clean.bam125

Sample: trimmed_DKO_R2.fastq.gz.sam.sort.clean.bam125

Sample: trimmed_HCT116_R1.fastq.gz.sam.sort.clean.bam125

Warning message:

In dba.multicore.init(DBA$config) :

Parallel execution unavailable: executing serially.

Can someone answer why I am continuously getting this error even when I set the paramenter bParallel=FALSE?

samples <- read.csv("sample.csv", sep=",")

compare <- dba(sampleSheet=samples)

compareCount <- dba.count(compare, bParallel=FALSE)


Thank you for your help in advance.


diffbind parallel • 321 views
ADD COMMENTlink modified 21 months ago by Rory Stark2.9k • written 21 months ago by ghosos0
Answer: DiffBind count warning
gravatar for Rory Stark
21 months ago by
Rory Stark2.9k
CRUK, Cambridge, UK
Rory Stark2.9k wrote:

Yes, this warning does happen on Windows only.

If this really annoys you, there is a workaround. You can set a configuration option to a specific value, as in the following example:

tamoxifen$config$parallelPackage <- 4

You won't see the warning anymore, but you will get an error if you try to run anything in parallel, so you should also set:

tamoxifen$config$RunParallel <- FALSE

after which you don't need to explicitly set bParallel=FALSE.




ADD COMMENTlink written 21 months ago by Rory Stark2.9k
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