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thomasvangurp / epiGBS

Code for working with epiGBS data
MIT License
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The loaded bed file has less columns than expected, check the correctness of column assignment (or the BED style option) #28

Closed mehmet-cay closed 11 months ago

mehmet-cay commented 11 months ago

Hi, I am trying to import my bed files for wgbs data.

Here my script:

data_dir <- "/vast/palmer/scratch/................." data_type <- "bs.bed.dir" sample_annotation_file <- file.path(data_dir, "sample.csv") analysis_dir <- "/vast/palmer/scratch/..............." report_dir <- file.path(analysis_dir, "reports") data_source <- c(data_dir, sample_annotation_file) result <- rnb.run.import(data.source = data_source, data.type = data_type, dir.reports = report_dir)

here is an error:

result <- rnb.run.import(data.source = data_source,

  • data.type = data_type,
  • dir.reports = report_dir) 2024-01-04 02:17:33 3.1 STATUS STARTED Loading Data 2024-01-04 02:17:33 3.1 INFO Number of cores: 1 2024-01-04 02:17:33 3.1 INFO Loading data of type "bs.bed.dir" 2024-01-04 02:17:33 3.1 STATUS STARTED Performing loading test 2024-01-04 02:17:33 3.1 INFO The first 10000 rows will be read from each data file 2024-01-04 02:17:33 3.1 INFO No column with file names specified: will try to find one 2024-01-04 02:17:33 3.1 STATUS STARTED Loading Data From BED Files 2024-01-04 02:17:35 3.1 STATUS STARTED Automatically parsing the provided sample annotation file 2024-01-04 02:17:35 3.1 STATUS Potential file names found in column 4 of the supplied annotation table 2024-01-04 02:17:35 3.1 STATUS COMPLETED Automatically parsing the provided sample annotation file 2024-01-04 02:17:35 3.1 INFO Reading BED file: /vast/palmer/scratch/................................................/Control-1-bloodAH7JG3DSX3L001.pair1.bed Error in FUN(X[[i]], ...) : The loaded bed file /vast/palmer/scratch/......................................../Control-1-bloodAH7JG3DSX3L001.pair1.bed has less columns than expected, check the correctness of column assignment (or the BED style option) In addition: Warning message: In read.table(file = file, header = header, sep = sep, quote = quote, : cols = 3 != length(data) = 6

Can you please help me?