diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index 830180df6cf1fcc057e39092649b96b23e09f8b1..235d1d64777ac0d785e104f99e2769e2d169eaea 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -11,10 +11,10 @@ if config["SeOrPe"] == "PE":
             config["<step_name>__accel_align_threads"]
         params:
             command = config["<step_name>__accel_align_PE_command"],
-            output_dir = config["results_dir"]+"/"+config["<step_name>__accel_align_SE_output_dir"],
+            output_dir = config["results_dir"]+"/"+config["<step_name>__accel_align_PE_output_dir"],
             #indexPrefix =  config["<step_name>__accel_align_index_output_dir"]+"/index",
             #/patho_index/indexName.fna.hash 
-            indexPrefix = lambda w, input: os.path.splitext([x for x in input.index ][1]),
+            indexPrefix = lambda w, input: os.path.splitext(input.index[0])[0],
             accel_align_seed_length = config["<step_name>__accel_align_seed_length"],
             accel_align_insert_size = config["<step_name>__accel_align_insert_size"],
             accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
@@ -52,7 +52,7 @@ elif config["SeOrPe"] == "SE":
             accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
             accel_align_alignment_free = "-x" if config["<step_name>__accel_align_alignment_free"] else "",
             #indexPrefix =  config["<step_name>__accel_align_index_output_dir"]+"/index",
-            indexPrefix = lambda w, input: os.path.splitext([x for x in input.index][1]),
+            indexPrefix = lambda w, input: os.path.splitext([x for x in input.index])[0],
         shell:
             "{params.command} "
             "-t {threads} "
diff --git a/tools/accel_align_index/accel_align_index.rule.snakefile b/tools/accel_align_index/accel_align_index.rule.snakefile
index 46e2bf1758931ee7dfbcb39727931c727b86304c..d78aae48606fe9abf49f8d81904d089567f25c6c 100755
--- a/tools/accel_align_index/accel_align_index.rule.snakefile
+++ b/tools/accel_align_index/accel_align_index.rule.snakefile
@@ -2,6 +2,10 @@ rule <step_name>__accel_align_index:
     input:
         **<step_name>__accel_align_index_inputs()
     output:
+       index = (
+            config["<step_name>__accel_align_index_output_dir"]+"/index",
+            config["<step_name>__accel_align_index_output_dir"]+"/index.hash",
+        )
         index = config["<step_name>__accel_align_index_output_dir"]+"/index.hash",
     log:
         config["results_dir"]+"/logs/" + config["<step_name>__accel_align_index_output_dir"] + "/index.log"
@@ -14,5 +18,5 @@ rule <step_name>__accel_align_index:
         "-l  {params.accel_align_index_kmers_length} "        
         "{input.genome_fasta} "
         "|& tee {log};"
-        "cp {input.genome_fasta}  {params.out_dir}/index "
-        "cp {input.genome_fasta}.hash  {params.out_dir}/index.hash "
+        "cp {input.genome_fasta}  {params.out_dir}/index; "
+        "mv {input.genome_fasta}.hash  {params.out_dir}/index.hash ;"