This command rows <- as.numeric(system(paste("wc -l < /path/myFile.txt",sep=""), TRUE)) works when used directly in R and when I put it inside a shell script and submit it to the cluster. This command columns <- as.numeric(system(paste("head -1 < /path/myFile.txt | wc -w",sep=""), TRUE)) works when used in R, however is not working when I submit it. I am using these commands to count the number of rows and columns on a large file. Any suggestions? Thanks, Juliet