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gagneurlab / OUTRIDER

OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
MIT License
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findEncodingDim running issues #36

Open runjin326 opened 3 years ago

runjin326 commented 3 years ago

Hello,

I am trying to implement the package for outlier detection and I am stuck on the findEncodingDim step.

I looked into previous issues and solutions and implemented the following - my machine has 6 cores but I am only allocating 5 since last time I used 6, my machine got hung up.

ncores <- 5
register(MulticoreParam(ncores, ncores*2, progressbar = TRUE))
ods<- findEncodingDim(ods, BPPARAM=bpparam(), params = seq(2,20,by=2))

But the issue is, the progress bar kept being at 0% for >5 hours and I am not sure whether it would go anywhere. The dataset I used has 24910 genes * 206 samples after FPKM filter.

Thanks!

runjin326 commented 3 years ago

So now I am running it on EC2 instances and am getting the following error message:

|                                                                      |   0%Error in result[[njob]] <- value : 
  attempt to select less than one element in OneIndex
Calls: lapply ... findEncodingDim -> bplapply -> bplapply -> bploop -> bploop.lapply
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result

@c-mertes

c-mertes commented 1 year ago

This could be related to https://github.com/Bioconductor/BiocParallel/issues/106 or to https://github.com/Bioconductor/BiocParallel/issues/237

Can you try the new BiocParallel version 1.32.5 and see if the error is gone? If the above does not help, can you try the fix mentioned here: https://github.com/gagneurlab/OUTRIDER/issues/26#issuecomment-686733038