diff --git a/main.nf b/main.nf
index ecfce36496f25b291c8bf1894674b63542c01dfc..963c260532e62d7fb63101ae6f355147fbf5f89d 100644
--- a/main.nf
+++ b/main.nf
@@ -978,7 +978,7 @@ process compartment_calling {
 
   script:
   """
-  cooltools genome binnify ${chrsize} ${res} > genome_bins.txt
+  cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
   cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt 
   cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
   awk -F"\t" 'NR>1{OFS="\t"; if(\$6==""){\$6=0}; print \$1,\$2,\$3,\$6}' ${sample}_compartments.cis.vecs.tsv | sort -k1,1 -k2,2n > ${sample}_compartments.cis.E1.bedgraph