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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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crash if run on large number of samples #80

Open dkhalenkw opened 2 years ago

dkhalenkw commented 2 years ago
  1. We need to run around 400 samples (each is RNA-seq data from one of the patients) but the FRASER crashes. (It runs ok with lower number of samples - <25).
  2. machine specifications:
    CPUs: 8 memory: 32849380 storage: /home total: 11T used: 2,7T free: 8,3T
  3. Programm is killed when running function countRNAData(). with the following error: Error in sendMaster(try(eval(expr, env), silent = TRUE), FALSE) : ignoring SIGPIPE signal Calls: countRNAData ... bploop.lapply -> .send_to -> .send_to -> -> sendMaster Error in sendMaster(try(eval(expr, env), silent = TRUE), FALSE) : ignoring SIGPIPE signal Calls: countRNAData ... bploop.lapply -> .send_to -> .send_to -> -> sendMaster

The parallelization should be turned on by the following code: if(.Platform$OS.type == "unix") { register(MulticoreParam(workers=min(10, multicoreWorkers()))) } else { register(SnowParam(workers=min(10, multicoreWorkers()))) }