Question: DiffBind count warning
0
gravatar for ghosos
19 months ago by
ghosos0
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 • 306 views
ADD COMMENTlink modified 19 months ago by Rory Stark2.8k • written 19 months ago by ghosos0
Answer: DiffBind count warning
0
gravatar for Rory Stark
19 months ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k 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:

data(tamoxifen_peaks)
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 19 months ago by Rory Stark2.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 100 users visited in the last hour