Trace Back Index error with gene_mapper.py and Warning message

[harsha rani]

Hi, I am trying to run ROSE using the following parameter ROSE_main.py -g HG38 -i H3K27ac_1.gff -r H3K27ac_1_sorted.bam -c Input_sorted.bam -o superenhancers -s 12500 -t 2000. The gff that i created was using the following command awk '{OFS="\t"; print $1, $4, ".", $2, $3, ".",".",".", $4}' H3k27ac_1_peaks.narrowPeak > H3K27ac_1.gff

I got all the output files except for the gene_mapper. The png and table.txt file is also created .

The program ran completely except for gene_mapper.py and i got a warning message as well Warning message:
In write.table(file = outputFile, superEnhancer, sep = "\t", quote = FALSE, :
appending column names to file
Warning message:
In write.table(file = outputFile, superEnhancer, sep = "\t", quote = FALSE, :
appending column names to file.

The annotation is not working with the output file somehow. I need help to resolve this as i am new to this tool