ChIPQC showed errors 'nnodes' must be >= 1
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Entering edit mode
8.3 years ago
lkw.wang • 0

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!

ChIP-Seq software-error next-gen • 2.0k views
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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)

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

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8.3 years ago

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

HTH

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