R read.tabe  line 5 did not have 2 elements

Reason:

there are special characters such as # in file

old_value    new_value
EZF2    ZNF444
EZF2    ZNF444
ZSCAN17    ZNF444
RIFK    RFK
CSTP1#    CPPED1
ENT3    SLC29A3
HCLAP    SLC29A3
HJCD    SLC29A3

Solution:

chromosomes <- read.csv(chromFile, sep = "\t", skip = 0, header = TRUE,

                        comment.char = "", check.names = FALSE)