Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution ha

Question

I've been trying to use copywriter to extract the copy number information of some exomes from mice (mm10) and kept encountering the same error:

Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted

    library("CopywriteR")
    library("BiocParallel")
    library("matrixStats")
    library("gtools")
    library("data.table")
    library("S4Vectors")
    library("chipseq")
    library("IRanges")
    library("Rsamtools")
    library("DNAcopy")
    library("GenomicAlignments")
    library("GenomicRanges")
    library("CopyhelpeR")
    library("GenomeInfoDb")
    library("futile.logger")

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

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

    path <- "/mnt/atgc-d1/drobles/ftalavera/copywriter_test"
    samples <- list.files(path = path, pattern = ".bam$", full.names = TRUE)
    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, "mm10_4_20kb"),
                 bp.param = bp.param)

I have tried everything in the troubleshooting section in github but I still can't figure out what is happening, Do you have any idea? I already submitted an issue on github but have no response.

I tried with the data from the SCLCBam package: https://github.com/PeeperLab/SCLCBam/releases

Here is the example I followed: https://bioconductor.riken.jp/packages/3.3/bioc/vignettes/CopywriteR/inst/doc/CopywriteR.pdf

I would really appreciate your help.