Question: bumphunter stalls on "Smoothing coefficients"
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gravatar for rasmus.rydbirk
4 months ago by
rasmus.rydbirk10 wrote:

I've been using bumphunter to get DMR and Blocks as defined in the ChAMP package (champ.DMR and champ.Block functions, respectively) on a MethylationEPIC data set (37 controls, 41 patients). Unfortunately, for both functions, it's stalling at:

[bumphunterEngine] Computing coefficients. [bumphunterEngine] Smoothing coefficients.

I've been running with at least 20 cores/100 GB memory for up to 99 hours. I've been trying R v. 3.5, 3.5.3, and 3.6. How can this smoothing take so long/any advice on what I should do? The last time, I tried with R v. 3.5 using ChAMP v. 2.12.4 (bumphunter v. 1.24.5). with standard code:

champ.DMR(beta=myNorm,
          pheno=myLoad$pd$Sample_Group,
          compare.group=NULL,
          arraytype="EPIC",
          method = "Bumphunter",
          minProbes=7,
          adjPvalDmr=0.05,
          cores=20,
          ## following parameters are specifically for Bumphunter method.
          maxGap=300,
          cutoff=NULL,
          pickCutoff=TRUE,
          smooth=TRUE,
          smoothFunction=loessByCluster,
          useWeights=FALSE,
          permutations=NULL,
          B=250,
          nullMethod="bootstrap")

Output:

[ Section 2:  Run DMR Algorithm Start ]

Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19
<< Find DMR with Bumphunter Method >>
20 cores will be used to do parallel Bumphunter computing.
According to your data set, champ.DMR() detected 11355 clusters contains MORE THAN 7 probes within300 maxGap. These clusters will be used to find DMR.

[bumphunterEngine] Parallelizing using 20 workers/cores (backend: doParallelMC, version: 1.0.14).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

The following object is masked from 'package:base':

    isFALSE

=>> PBS: job killed: walltime 356440 exceeded limit 356400

I will add sessionInfo() later, server is busy right now.

bumphunter champ • 125 views
ADD COMMENTlink modified 4 months ago by Yuan Tian110 • written 4 months ago by rasmus.rydbirk10
Answer: bumphunter stalls on "Smoothing coefficients"
2
gravatar for Yuan Tian
4 months ago by
Yuan Tian110
University College London
Yuan Tian110 wrote:

Someone in my lab reported similar error before. But I can not replicate it on my server or laptop. So I eventually solved it by ask her setting cores=1, means not use parallel.

Thus, I suspect the reason is doParallel package.

Best Yuan Tian

rasmus.rydbirk [bioc] noreply@bioconductor.org 于 2019年5月20日周一 下午3:02写道:

ADD COMMENTlink written 4 months ago by Yuan Tian110

Hi Yuan

Thanks for quick reply. I will try overnight with 1 or 4 cores to see if I can get it to work. Can you give me an estimate of running time for this (both DMRs and blocks) when only using one core? Are we talking 10 min/1 h/1 day?

/Rasmus

Fra: Yuan Tian [bioc] noreply@bioconductor.org Sendt: 20. maj 2019 16:15 Til: Rasmus Rydbirk rasmus.rydbirk@regionh.dk Emne: [bioc] A: bumphunter stalls on "Smoothing coefficients"

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org

User Yuan Tianhttps://support.bioconductor.org/u/13904/ wrote Answer: bumphunter stalls on "Smoothing coefficients"https://support.bioconductor.org/p/121241/#121242:

Someone in my lab reported similar error before. But I can not replicate it on my server or laptop. So I eventually solved it by ask her setting cores=1, means not use parallel.

Thus, I suspect the reason is doParallel package.

Best Yuan Tian

rasmus.rydbirk [bioc] noreply@bioconductor.orgnoreply@bioconductor.org 于 2019年5月20日周一 下午3:02写道:

ADD REPLYlink written 4 months ago by rasmus.rydbirk10

Sorry, I can't estimate it well, cause on my server and computer it works well...so I normally only use parallel settings.

Best Yuan Tian

rasmus.rydbirk [bioc] noreply@bioconductor.org 于 2019年5月20日周一 下午3:18写道:

ADD REPLYlink written 4 months ago by Yuan Tian110

I can confirm multi-thread problems: Running with 1 core took 10-25 min for both functions. Thanks!

ADD REPLYlink written 4 months ago by rasmus.rydbirk10
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