thomasKuilman
commented
7 years ago I believe this post should fix your problem. Alternatively you may want to check the integrity of your bam files using samtools (e.g. $ samtools view -h BAMFILE | less). You should get an error message if your bam file is corrupted.
Hi-
I run CopyWrite R, but received the following error:
invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘RNGseed’ must be length 1 invalid class “MulticoreParam” object: 2: ‘timeout’, ‘log’ must be length 1 starting worker for localhost:11695 'BiocParallel' did not register default BiocParallelParams: invalid class “MulticoreParam” object: 1: ‘cluster’, ‘.clusterargs’, ‘RNGseed’ must be length 1 invalid class “MulticoreParam” object: 2: ‘timeout’, ‘log’ must be length 1 Warning message: In doTryCatch(return(expr), name, parentenv, handler) : space '1' not in BAM header Warning message: In doTryCatch(return(expr), name, parentenv, handler) : space '1' not in BAM header Error in .Method(..., deparse.level = deparse.level) : number of rows of matrices must match (see arg 2) Calls: CopywriteR ... f -> standardGeneric -> eval -> eval -> eval -> .Method In addition: Warning message: In doTryCatch(return(expr), name, parentenv, handler) : space '1' not in BAM header Execution halted
Could you help me found out the reason? Thanks!
Here is my code:
library("CopywriteR") library("CopyhelpeR") setwd("C:/Users/site_li/Documents/WES/data") data.folder <- tools::file_path_as_absolute(file.path(getwd()))
preCopywriteR(output.folder=file.path(data.folder), bin.size=20000, ref.genome="hg19", prefix="")
list.dirs(path = file.path(data.folder), full.names = FALSE) list.files(path = file.path(data.folder, "hg19_20kb"), full.names = FALSE) load(file = file.path(data.folder, "hg19_20kb", "blacklist.rda")) blacklist.grange
load(file=file.path(data.folder, "hg19_20kb", "GC_mappability.rda")) GC.mappa.grange[1001:1011]
bp.param <- SnowParam(workers = 12, type ="SOCK") bp.param
path <- c("C:/Users/site_li/Documents/WES/data") samples <- list.files(path=path, pattern="tumor.bam$", full.names=TRUE) controls <- list.files(path=path, pattern="control.bam$", 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, "hg19_20kb"), bp.param = bp.param)