Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution halted
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@87122f6e
Last seen 7 days ago
Mexico

Hi,

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 -> <Anonymous> Execution halted

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 would really appreciate your help.

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)
CopywriteR CopyhelpeR • 264 views
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What is your sessionInfo()?

Please note that CopywriteR was removed from Bioconductor in April 2023; it was last available in Bioconductor 3.16.

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Here is the sessionInfo():

R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /cm/shared/apps/r/3.6.1-studio/lib64/R/lib/libRblas.so LAPACK: /cm/shared/apps/r/3.6.1-studio/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] futile.logger_1.4.3 CopyhelpeR_1.0.2
[3] DNAcopy_1.60.0 chipseq_1.36.0
[5] ShortRead_1.44.3 GenomicAlignments_1.22.1
[7] SummarizedExperiment_1.16.1 DelayedArray_0.12.2
[9] Biobase_2.46.0 Rsamtools_2.2.3
[11] Biostrings_2.54.0 XVector_0.26.0
[13] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
[15] IRanges_2.20.2 S4Vectors_0.24.3
[17] BiocGenerics_0.32.0 data.table_1.12.8
[19] gtools_3.8.2 matrixStats_0.56.0
[21] CopywriteR_2.9.0 BiocParallel_1.20.1

loaded via a namespace (and not attached): [1] zlibbioc_1.32.0 lattice_0.20-38 jpeg_0.1-8.1
[4] hwriter_1.3.2.1 tools_3.6.1 grid_3.6.1
[7] png_0.1-7 latticeExtra_0.6-29 lambda.r_1.2.4
[10] Matrix_1.2-18 GenomeInfoDbData_1.2.2 formatR_1.7
[13] RColorBrewer_1.1-2 futile.options_1.0.1 bitops_1.0-6
[16] RCurl_1.98-1.1 compiler_3.6.1

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