DiffBind error with background=TRUE in dba.normalize?
1
0
Entering edit mode
Victor • 0
@Victor-24463
Last seen 3.8 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
ADD COMMENT
1
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 11 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
ADD COMMENT

Login before adding your answer.

Traffic: 695 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6