I'm trying to use CopywriteR to identify copy number alterations from .bam files, obtained using whole exome sequencing on a set of 30 human cancer tissues, without matched control. I've followed the vignette in bioconductor. However, the vignette indicates the code should create a directory named "CNAprofiles" that contains several files, including "read_counts.txt" and "CopywriteR.log." However, when I run the code, it creates a "CNAprofiles" directory, but it only contains "CopywriteR.log" and another directory titled "BamBaiPeaksFiles," which contains intermediary files titled XXXX.properreads.bam and XXXX.properreads.bam.bai. It doesn't create the "read_counts.txt" file, which is what I need.

I get no errors.

My code is below. It follows the vignette as closely as possible, vignette found here: https://bioconductor.org/packages/release/bioc/vignettes/CopywriteR/inst/doc/CopywriteR.pdf

Does anyone have any suggestion for what I'm doing wrong? Many thanks.

Code should be placed in three backticks as shown below

setwd("/hpc/.../my.bams") #this directory contains my .bam files

data.folder <- tools::file_path_as_absolute(file.path(getwd()))

preCopywriteR(output.folder = file.path(data.folder), bin.size = 20000,, ref.genome = "hg19")

load(file = file.path(data.folder, "hg19_20kb", "blacklist.rda"))

bp.param <- SnowParam(workers = 1, type = "SOCK")

samples <- list.files(pattern = ".bam$", full.names = TRUE)

#make each sample its own control
controls <- samples

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, keep.intermediary.files=FALSE)