DiffBind error with background=TRUE in dba.normalize?
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Victor • 0
@Victor-24463
Last seen 3.9 years ago

Hello,

I tried DiffBind (v3.0.9) to find DE binding sites from ChIP-seq data. When I used "dba.normalize" with "background=TRUE". It ended up with this error:


DB = dba.normalize(DB, normalize=DBA_NORM_NATIVE, background=TRUE)
Generating background bins...
Error in .local(x, ...) : 
  cannot create 160 workers; 125 connections available in this session 

sessionInfo( )

It seems that my server has 160 cpu cores, and BiocParallel or parallel embeded in DiffBind aquire all the cpu cores in running the task, while the R session only support up to 125 cores.

I'm woundering if you can provide any solution to this issue?

Thanks very much!

WS

BiocParallel DiffBind parallel • 1.7k views
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Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 27 days ago
Cambridge, UK

You can set the number of cores that DiffBind uses as a configuration option before calling dba.normalize():

DB$config$cores <- 32
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