YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
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invalid DB file #225

Open hanguojun007 opened 9 months ago

hanguojun007 commented 9 months ago

Hi , I have a function anno_plot ,when i use it in foreach, i produce a error. function :

anno_plot <- function(bed, txDb) {
    peak <- ChIPseeker::readPeakFile(bed)
    peakAnno <- ChIPseeker::annotatePeak(
        peak,
        tssRegion = c(-3000, 3000),
        TxDb = txDb
    )
}

foreach code:

cl <- makeCluster(length(bed_files))
registerDoParallel(cl)
mat_df_all <- foreach(bed = bed_files, .packages = c("ChIPseeker", "AnnotationDbi", "IRanges", "GenomeInfoDb"), .verbose = TRUE) %dopar% anno_plot(bed, txdb)
stopCluster(cl)

error:

ot(bed, txdb)
discovered package(s): 
automatically exporting the following variables from the local environment:
  anno_plot, txdb 
explicitly exporting package(s): ChIPseeker, AnnotationDbi, IRanges, GenomeInfoDb
numValues: 2, numResults: 0, stopped: TRUE
got results for task 1
accumulate got an error result
numValues: 2, numResults: 1, stopped: TRUE
returning status FALSE
got results for task 2
numValues: 2, numResults: 2, stopped: TRUE
not calling combine function due to errors
returning status TRUE
Error in anno_plot(bed, txdb) : task 1 failed - "invalid DB file"