diff --git a/README.md b/README.md
index be2e347..eb675c8 100644
--- a/README.md
+++ b/README.md
@@ -230,7 +230,6 @@ Create `run_snakemake.sh`:
 #SBATCH --partition=medium
 #SBATCH --cpus-per-task=4
 #SBATCH --mem=8G
-#SBATCH --time=48:00:00
 #SBATCH --output=snakemake-%j.out
 #SBATCH --error=snakemake-%j.err
 
diff --git a/workflow/rules/fastK_merged.smk b/workflow/rules/fastK_merged.smk
deleted file mode 100644
index 454857c..0000000
--- a/workflow/rules/fastK_merged.smk
+++ /dev/null
@@ -1,40 +0,0 @@
-# This rule generates a FastK table needed to run merquryFK
-
-
-rule fastk_merged:
-    wildcard_constraints:
-        reads_type="merged",
-    input:
-        merged_in=f"{input_dir}" + "{sample}/{sample}_merge.fq.gz",
-    output:
-        ktab=f"{output_dir}" + "{reads_type}/fastk/{sample}/fastk_table.ktab",
-        hist=f"{output_dir}" + "{reads_type}/fastk/{sample}/fastk_table.hist",
-    params:
-        k=config["fastk"]["k"],
-        result_prefix=lambda wildcards, output: os.path.splitext(output.ktab)[0],
-        t=config["fastk"]["t"],
-        memory_gb=lambda wildcards, resources: resources.mem_mb // 1024,
-        temp_dir=lambda wildcards, output: os.path.join(
-            os.path.dirname(output.ktab), "temp"
-        ),
-    threads: get_low_threads
-    resources:
-        mem_mb=get_low_mem,
-        partition=config["low"]["partition"],
-    log:
-        "logs/{sample}/fastk_{reads_type}.log",
-    benchmark:
-        "benchmark/{sample}/fastk_{reads_type}.txt"
-    conda:
-        "../envs/merquryFK.yaml"
-    container:
-        "docker://quay.io/biocontainers/merquryfk:1.1.3--h71df26d_0"
-    shell:
-        """
-        mkdir -p {params.temp_dir}
-
-        echo "Running FastK with the following command:" >> {log} 2>&1
-        echo "FastK -v -T{threads} -k{params.k} -M{params.memory_gb} {input.merged_in} -N{params.result_prefix} -t{params.t} -P{params.temp_dir}" >> {log} 2>&1
-        FastK -v -T{threads} -k{params.k} -M{params.memory_gb} {input.merged_in} -N{params.result_prefix} -t{params.t} -P{params.temp_dir} >> {log} 2>&1
-        rm -rf {params.temp_dir}  # clean up temporary directory
-        """
diff --git a/workflow/rules/select_best_assembly.smk b/workflow/rules/select_best_assembly.smk
index 361b53f..4e5e22d 100644
--- a/workflow/rules/select_best_assembly.smk
+++ b/workflow/rules/select_best_assembly.smk
@@ -9,11 +9,14 @@ rule select_best_assembly:
         ),
         report=f"{output_dir}" + "quast/{sample}/report.txt",
     output:
-        best_assemblies_dir=directory(f"{output_dir}" + "best_assembly/{sample}/"),
         assembly=f"{output_dir}" + "best_assembly/{sample}/{sample}_best_assembly.fa",
     params:
         sample="{sample}",
-        results_dir=output_dir,
+        results_dir=lambda w, output: os.path.dirname(
+            os.path.dirname(os.path.dirname(output.assembly))
+        )
+        + "/",
+        best_assemblies_dir=lambda w, output: os.path.dirname(output.assembly) + "/",
     threads: 1
     resources:
         mem_mb=get_very_low_mem,
@@ -29,6 +32,6 @@ rule select_best_assembly:
     shell:
         """
         echo "Running the script as follows:" >> {log} 2>&1
-        echo "workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {output.best_assemblies_dir}" >> {log} 2>&1
-        workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {output.best_assemblies_dir} >> {log} 2>&1
+        echo "workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {params.best_assemblies_dir}" >> {log} 2>&1
+        workflow/scripts/select_best_assembly.sh -s {params.sample} -r {params.results_dir} -o {params.best_assemblies_dir} >> {log} 2>&1
         """