bedtools intersect generated empty files

[qicaibiology]

Hi: I have used bedtools to do intersect between bed6 files and the bed I generated from csv. At first I got the following error: $ awk -F '[,]' 'NR>=2{print $2, $3, $4,$5,".", $7}' OFS='\t' All_retained_intron.csv > All_retained_intron.bed $ bedtools intersect -a GRCm38_genes_introns_bed6.bed -b All_retained_intron.bed > IR_in_intron.bed

• WARNING: File GRCm38_genes_introns_bed6.bed has inconsistent naming convention for record: CHR_MG4180_PATCH 109649750 109650579 ENSMUST00000203001_intron 1 +

• WARNING: File GRCm38_genes_introns_bed6.bed has inconsistent naming convention for record: CHR_MG4180_PA TCH 109649750 109650579 ENSMUST00000203001_intron 1 +

My search brought me here, so I changed my code following people's instructions here: $ bedtools intersect -nonamecheck -u -s -a All_retained_intron.bed -b GRCm38_genes_intron_bed6.bed > IR_in_intron.bed

This time there is no error, but the generated file contains nothing!

Can anyone help me on this?

Thanks