Index out of Range closestGene = allEnhancerGenes[distList.index(min(distList))] Traceback (most recent call last):ROSE_geneMapper.py

[Former user]

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

gff file looks like this:

chr1 HCT_H3k27ac_1_peak_1 . 28904 29883 . . . HCT_H3k27ac_1_peak_1 chr1 HCT_H3k27ac_1_peak_2 . 199305 200504 . . . HCT_H3k27ac_1_peak_2 chr1 HCT_H3k27ac_1_peak_3 . 737355 737637 . . . HCT_H3k27ac_1_peak_3 chr1 HCT_H3k27ac_1_peak_4 . 777918 778620 . . . HCT_H3k27ac_1_peak_4 chr1 HCT_H3k27ac_1_peak_5 . 778849 780275 . . . HCT_H3k27ac_1_peak_5 chr1 HCT_H3k27ac_1_peak_6 . 826766 827943 . . . HCT_H3k27ac_1_peak_6 chr1 HCT_H3k27ac_1_peak_7 . 958890 959239 . . . HCT_H3k27ac_1_peak_7 chr1 HCT_H3k27ac_1_peak_8 . 959369 961143 . . . HCT_H3k27ac_1_peak_8 chr1 HCT_H3k27ac_1_peak_9 . 965664 967415 . . . HCT_H3k27ac_1_peak_9 chr1 HCT_H3k27ac_1_peak_10 . 976285 976508 . . . HCT_H3k27ac_1_peak_10

Could you please let me know what could be the mistake.