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kdkorthauer / dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
MIT License
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Error: 'bplapply' receive data failed: error reading from connection #7

Closed lulizou closed 6 years ago

lulizou commented 6 years ago

Hi,

I'm trying to run dmrseq on a cluster, here is the command I ran:

regions <- dmrseq(bs = all, testCovariate = "type", parallel = T)

and the output/error:

Condition T2D vs NGT
Parallelizing using 54 workers/cores (backend: BiocParallel).

Detecting candidate regions with coefficient larger than 0.1 in magnitude.
.....Computing coefficients.
.....Smoothing coefficients.
..........Done Smoothing Chromosome chr1. Took 1.21 minutes
..........Done Smoothing Chromosome chr2. Took 1.09 minutes
..........Done Smoothing Chromosome chr3. Took 0.86 minutes
..........Done Smoothing Chromosome chr4. Took 0.82 minutes
..........Done Smoothing Chromosome chr5. Took 0.81 minutes
..........Done Smoothing Chromosome chr6. Took 1.02 minutes
..........Done Smoothing Chromosome chr7. Took 0.88 minutes
..........Done Smoothing Chromosome chr8. Took 0.78 minutes
..........Done Smoothing Chromosome chr9. Took 0.73 minutes
..........Done Smoothing Chromosome chr10. Took 0.78 minutes
..........Done Smoothing Chromosome chr11. Took 0.79 minutes
..........Done Smoothing Chromosome chr12. Took 0.75 minutes
..........Done Smoothing Chromosome chr13. Took 0.55 minutes
..........Done Smoothing Chromosome chr14. Took 2.01 minutes
..........Done Smoothing Chromosome chr15. Took 0.58 minutes
..........Done Smoothing Chromosome chr16. Took 0.66 minutes
..........Done Smoothing Chromosome chr17. Took 0.77 minutes
..........Done Smoothing Chromosome chr18. Took 0.53 minutes
..........Done Smoothing Chromosome chr19. Took 0.68 minutes
..........Done Smoothing Chromosome chr20. Took 0.55 minutes
..........Done Smoothing Chromosome chr21. Took 0.43 minutes
..........Done Smoothing Chromosome chr22. Took 0.52 minutes
.....Evaluating 156 candidate regions.
Error: 'bplapply' receive data failed:
  error reading from connection

Any help would be greatly appreciated. Thanks!

LKremer commented 6 years ago

I've encountered this error before when I used too many parallel cores and ran out of RAM. In my experience, you have to be very modest with the number of cores you use, maybe try something like four. It shouldn't take too long anyways.

lulizou commented 6 years ago

Thanks! Works fine with 1 core.