I recently tried to use CopywriteR in Microsoft Azure cloud - Windows Server Datacenter Virtual MachineĀ (128 RAM and 16 cores) with R 3.3.2. Also my input data files: normal 12.67GB, tumor 11GB
I received the following error:
Error: 'bplapply' receive data failed: error reading from connection
Can you suggest a work around? Maybe too many bam lines are being read at once?
Here is my code:
library("CopywriteR") library("CopyhelpeR") setwd("C:/Users/m/Desktop/share/data") data.folder <- tools::file_path_as_absolute(file.path(getwd())) preCopywriteR(output.folder=file.path(data.folder), bin.size=20000, ref.genome="hg38", prefix="chr") list.dirs(path=file.path(data.folder), full.names=FALSE) list.files(path=file.path(data.folder, "hg38_20kb_chr"), full.names=FALSE) load(file=file.path(data.folder, "hg38_20kb_chr", "blacklist.rda")) blacklist.grange load(file=file.path(data.folder, "hg38_20kb_chr", "GC_mappability.rda")) GC.mappa.grange[1001:1011] bp.param <- SnowParam(workers = 15, type ="SOCK") bp.param path <- c("C:/Users/m/Desktop/share/data") samples <- list.files(path=path, pattern="tumor.bam$", full.names=TRUE) controls <- list.files(path=path, pattern="normal.bam$", full.names=TRUE) sample.control <- data.frame(samples,controls) CopywriteR(sample.control = sample.control, destination.folder = file.path(data.folder), reference.folder = file.path(data.folder, "hg38_20kb_chr"), bp.param = bp.param)