Replace test.txt with input.txt.

library(data.table)
geneConv <- function(x) {
    df <- fread("test.txt")
    output=df[gene_name==x,.(gene_id)]
    return(output)
}
geneConv("AB")

See if you can take fread function out. This is because every time, you want to search a gene ID, it has to execute fread and this affects the performance. Try something like this:

df <- fread("test.txt")
geneConv <- function(x) {
    output=df[gene_name==x,.(gene_id),nomatch=NA]
    return(output)
}

however, I would suggest to use this:

geneConv <- function(x) {
+     output=df[gene_name %in% x ,.(gene_id)]
+     return(output)
+     }
> 
> geneConv(c("AB","CD","ABC"))
   gene_id
1: ENSG001
2: ENSG002