diff --git a/src/mbelari_count.slurm b/src/mbelari_count.slurm
index 0ff67521f0e9a1f09db588400da0d9a33758d926..13ecc87f10fa039b92a48ca2a871601681e47f76 100644
--- a/src/mbelari_count.slurm
+++ b/src/mbelari_count.slurm
@@ -10,9 +10,9 @@
 
 cd /scratch/Bio/lmodolo/kmer_diff/
 
-alias kmdiff="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
 WORK=$(pwd)
 
 # kmdiff count
-kmdiff count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32
+${KMDIFF} count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32
 
diff --git a/src/mlongespiculosa_count.slurm b/src/mlongespiculosa_count.slurm
index bb33009c2dcfb8419e9a83e8686f2f68f449819b..36b8853eaa13be8a3f23699a06465bff7d20cb7a 100644
--- a/src/mlongespiculosa_count.slurm
+++ b/src/mlongespiculosa_count.slurm
@@ -10,8 +10,8 @@
 
 cd /scratch/Bio/lmodolo/kmer_diff/
 
-alias kmdiff="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
 WORK=$(pwd)
 
 # kmdiff count
-kmdiff count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
+${KMDIFF} count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
diff --git a/src/mspiculigera_count.slurm b/src/mspiculigera_count.slurm
index be4db3a5af2fdc7a26f6a278fbd5834606b06956..7716bd6322b410f91a4d71889b6c7b9de55ad781 100644
--- a/src/mspiculigera_count.slurm
+++ b/src/mspiculigera_count.slurm
@@ -11,8 +11,8 @@
 
 cd /scratch/Bio/lmodolo/kmer_diff/
 
-alias kmdiff="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
 WORK=$(pwd)
 
 # kmdiff count
-kmdiff count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 32
+${KMDIFF} count -f ${WORK}/data/sample_mspiculigera.csv -d ${WORK}/results/mspiculigera_counts/ -t 32