I got error in running chromosome_binless.R script

[ajaykumarsaw]

Hi, I, Ajay Kumar Saw, a research scholar in IISER, Pune, India. I am trying to run binless protocol. I successful run preprocessing.R, optimized_binless.R and fast_binless.R but I stuck in "chromosome_binless.R". I need your help to sort out this issue. Thank you in advance for your help.

####### R version information ################################################

R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-conda_cos6-linux-gnu (64-bit)

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I got error while running "chromosome_binless.R" script which is given below:-

library(binless) ajay1 <- load("example/rao_HiCall_SEMA3C_csnorm.RData") args=commandArgs(trailingOnly=TRUE) args = c("5000","ajay1") args [1] "5000" "ajay1" if (length(args)<= 1 || length(args) > 3) stop(paste0("\nargs: resolution sample1 [sample2]\n")) resolution=as.integer(args[1]) sample=args[2] #provide path to csdata object in RData format if (length(args)==3) { sample2 = args[3] } else { sample2 = NA } ncores = 8 far.cutoff=10e6 out_prefix="chromosome_binless" zoom_region="full" chromosome_binless(sample, sample2=sample2, zoom_region=zoom_region, ncores=ncores, base.res=resolution, far.cutoff=far.cutoff, out_prefix=out_prefix) Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection In addition: Warning message: In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file 'ajay1', probable reason 'No such file or directory'

[yannickspill]

Hi Ajay, in sample, you have to provide the path to the input file, not the name of the loaded object.