methRead takes too long

Question

[CTLong]

Hi,

I have been pre-processing my RRBS data with Bismark for which I have obtained bam files and coverage files that could be loaded into MethylKit for downstream analysis. However, the methRead function ran more than half a day on my HPCC cluster where I have 28 samples with coverage files as input. I did not receive any error messages. Below is my code, may I ask whether this is normal, or is my process stalled in the background without any messages popping up?

library(methylKit)
library(data.table)

coverage_files <- list.files(path = "/home/lab/bismark_methylation", pattern = "\\.cov.gz$")
coverage_files <- paste0("/home/lab/bismark_methylation/", coverage_files)
coverage_fread <- lapply(coverage_files, fread)
meta <- read_excel("/home/lab/supplementary_table.xlsx")
meta <- meta[match(substr(coverage_files , start = 57 , stop = 66), meta$Sample.Name),]

myobj <- methRead(list(coverage_fread),sample.id=meta$Sample.Name,pipeline = "bismarkCoverage", assembly="hg18", treatment = list(ifelse(meta$type%in% "disease", 1, 0)),context = "CpG")
saveRDS(myobj, file = "/home/lab/methRead.RDS")