mcapply:所有计划的核心在用户代码中遇到错误

时间:2016-09-01 20:03:00

标签: r parallel-processing mclapply

以下是我的代码。我正在尝试获取以.idat结尾的所有文件(~20000)的列表,并使用函数illuminaio::readIDAT读取每个文件。

library(illuminaio)
library(parallel)
library(data.table)

# number of cores to use
ncores = 8

# this gets all the files with .idat extension ~20000 files
files <- list.files(path = './',
                    pattern = "*.idat",
                    full.names = TRUE)

# function to read the idat file and create a data.table of filename, and two more columns
# write out as csv using fwrite
get.chiptype <- function(x)
{
  idat <- readIDAT(x)
  res <- data.table(filename = x, nSNPs = nrow(idat$Quants), Chip = idat$ChipType)
  fwrite(res, file.path = 'output.csv', append = TRUE)
}

# using mclapply call the function get.chiptype on all 20000 files.
# use 8 cores at a time
mclapply(files, FUN = function(x) get.chiptype(x), mc.cores = ncores)

在阅读和写入有关1200个文件的信息后,我收到以下消息:

Warning message:
In mclapply(files, FUN = function(x) get.chiptype(x), mc.cores = ncores) :
  all scheduled cores encountered errors in user code

我该如何解决?

0 个答案:

没有答案