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GreenleafLab / ChrAccR

Analyzing chromatin accessibility data in R
https://GreenleafLab.github.io/ChrAccR/
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quantile normalization error in vignette #15

Closed arugula2388 closed 1 year ago

arugula2388 commented 1 year ago

quantile normalization for all region types

dsa_qnorm <- transformCounts(dsa, method="quantile") Last executed at 2023-04-27 10:17:47 in 21ms 2023-04-27 10:17:47 7.9 STATUS STARTED Performing quantile normalization 2023-04-27 10:17:47 7.9 STATUS Region type: promoters_gc_protein_coding Error in preprocessCore::normalize.quantiles(ChrAccR::getCounts(.object, : ERROR; return code from pthread_create() is 22

Traceback:

  1. transformCounts(dsa, method = "quantile")
  2. transformCounts(dsa, method = "quantile")
  3. .local(.object, ...)
  4. preprocessCore::normalize.quan
arugula2388 commented 1 year ago

traceback

  1. transformCounts(dsa, method = "quantile")
  2. transformCounts(dsa, method = "quantile")
  3. .local(.object, ...)
  4. preprocessCore::normalize.quantiles(ChrAccR::getCounts(.object, . rt, asMatrix = TRUE))
demuellae commented 1 year ago

Looks like a parallelization issue in preprocessCore. Could you try to install it manually like in these threads? https://support.bioconductor.org/p/122925/ https://github.com/Bioconductor/bioconductor_docker/issues/22

arugula2388 commented 1 year ago

Resolved with the above advice; thanks!!