diff --git a/notebooks/slurm_scripts/launch_BWA.slurm b/notebooks/slurm_scripts/launch_BWA.slurm
index 6fd419ba9bcfa41591ca5d8eb5a0705de9ab7b59..0484fca5cc3499afaaf34039feecf019d5ca33d9 100644
--- a/notebooks/slurm_scripts/launch_BWA.slurm
+++ b/notebooks/slurm_scripts/launch_BWA.slurm
@@ -1,7 +1,7 @@
 #!/bin/bash 
 
 #SBATCH --job-name=BWA
-#SBATCH --cpus-per-task=1
+#SBATCH --cpus-per-task=2
 #SBATCH --mem-per-cpu=4G
 #SBATCH --output=BWA.o
 #SBATCH --error=BWA.e
diff --git a/notebooks/slurm_scripts/launch_bamqc.slurm b/notebooks/slurm_scripts/launch_bamqc.slurm
index 42919a9555bcbb285326e96afd14f1849eb777a5..c100118c32bf41af82f64ed54d0d368891940eb9 100644
--- a/notebooks/slurm_scripts/launch_bamqc.slurm
+++ b/notebooks/slurm_scripts/launch_bamqc.slurm
@@ -4,4 +4,4 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
 
-singularity exec /home/container.img qualimap bamqc -bam ERR760779.dedup.realigned.bam -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc
+singularity exec /home/container.img qualimap bamqc -bam ERR760779.dedup.bam  -sd -sdmode 1 -outdir . -outfile ERR760779_bamqc
diff --git a/notebooks/slurm_scripts/launch_mpileup.slurm b/notebooks/slurm_scripts/launch_mpileup.slurm
index aca1de106c3dfa65a4beb45dfcc0f0a65d481aa8..d737accc19399e483851c7fdad071fd3d8323e6a 100644
--- a/notebooks/slurm_scripts/launch_mpileup.slurm
+++ b/notebooks/slurm_scripts/launch_mpileup.slurm
@@ -4,5 +4,5 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --mem-per-cpu=4G
 
-singularity exec /home/container.img samtools mpileup -ABQ0 -q 20 -f ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779.dedup.realigned.bam > ERR760779.pileup
+singularity exec /home/container.img samtools mpileup -ABQ0 -q 20 -f ~/Workshop_SA/notebooks/reference_genome/MTB_ancestor_reference.fasta ERR760779.dedup.bam > ERR760779.pileup