ChIPQC showed errors 'nnodes' must be >= 1

Question

[lkw.wang]

When I used ChIPQC, I followed the manuals to construct a sample sheet (name is examplefile.csv), and then run:

>a <- read.csv("examplefile.csv")
>b = aa = ChIPQC(a, annotation=NULL)
air_k14_2 air_k14_2 air1   1 bed
air_k14_8 air_k14_8 air1   2 bed
air_k23_3 air_k23_3 air1   1 bed
air_k23_9 air_k23_9 air1   2 bed
air_k9_25 air_k9_25 air1   1 bed
air_k9_27 air_k9_27 air1   2 bed
C2H4_k14_5 C2H4_k14_5 C2H4-1   1 bed
C2H4_k14_11 C2H4_k14_11 C2H4-1   2 bed
C2H4_k23_6 C2H4_k23_6 C2H4-1   1 bed
C2H4_k23_12 C2H4_k23_12 C2H4-1   2 bed
C2H4_k9_26 C2H4_k9_26 C2H4-1   1 bed
C2H4_k9_28 C2H4_k9_28 C2H4-1   2 bed
Computing metrics for 16 samples...
Error in (function (nnodes = getOption("mc.cores", 2L), ...)  :
  'nnodes' must be >= 1**

When I use the same examplefile.csv file for DiffBind analysis, it works very well.

So, I don't know why the ChIPQC doesn't work.

Any help would be appreciated!

[Ying W]

Looks like it might have to do with you running ChIPQC in a non-multicore environment. You could try re-running and specifying more cores. Also, for bioconductor related questions, you would get a quicker response here: https://support.bioconductor.org/ (make sure you tag your question the the package that you are having problems with)

[lkw.wang]

Thank you very much for your reply. I used the detectCores function to determine I am using a multi-core environment. I will refer to the forum you suggested though. Thanks again.

>detectCores()
[1] 8
> detectCores(logical = FALSE)
[1] 4

[lkw.wang]

Thanks for your answer! I will learn how to define the cpu numbers in R.

Answer 1

[Sukhi Singh]

As Ying said and I speculate the same, either the number of CPUs are not defined before running the above function or the value is not increase from 1 (to have it a parallel computing environment)

Check the function here

parallel R package is throwing that error.

Check how to allocate/assign CPUs to R before running the program. detectCores() just tells you how many you have

Check the snow package and makeCluster function.

This will get you started

• https://wiki.hpcc.msu.edu/display/hpccdocs/R
• https://cran.r-project.org/web/views/HighPerformanceComputing.html
• http://dirk.eddelbuettel.com/papers/useR2010hpcTutorial.pdf

HTH