diff --git a/input/sampledata.txt b/input/sampledata.txt
index bd6cc3e..f3b2c1e 100644
--- a/input/sampledata.txt
+++ b/input/sampledata.txt
@@ -1,5 +1,4 @@
 SampleName	SampleID	AssemblyGroup	FastqFile
-HN008_subsampled	HN008	samplegroup1	HN008/HN008_subsampled
 HN009_subsampled	HN009	samplegroup2	HN009_subsampled
 HN016_subsampled	HN016	samplegroup1	HN016_subsampled
 HN036_subsampled	HN036	samplegroup1	HN036_subsampled
diff --git a/rules/02-trim.smk b/rules/02-trim.smk
index 7459a49..0288ac9 100644
--- a/rules/02-trim.smk
+++ b/rules/02-trim.smk
@@ -71,8 +71,8 @@ rule trimmomatic:
                           "02-trim",\
                           "{sample}_2.unpaired.fastq.gz")
     log:
-        err = os.path.join(OUTPUTDIR, "logs",\ 
-                           "01-setup", "02-trim",\ 
+        err = os.path.join(OUTPUTDIR, "logs",\
+                           "01-setup", "02-trim",\
                            "PE_{sample}_err.log"),
         out = os.path.join(OUTPUTDIR, "logs",\
                            "01-setup", "02-trim",\
diff --git a/rules/11-SWAM.smk b/rules/11-SWAM.smk
index b1da141..895f365 100644
--- a/rules/11-SWAM.smk
+++ b/rules/11-SWAM.smk
@@ -41,9 +41,9 @@ rule merge_all:
         '''
         echo "" > {output}
         for assemblyfile in {params.assemblyfiles}; do
-            currvar=$(echo $assemblyfile | rev | cut -f1 -d\/ | rev)
+            currvar=$(echo $assemblyfile | rev | cut -f1 -d\\/ | rev)
             sed 's/>.*/&_'"$currvar"'/' $assemblyfile >> {output}
         done
         #cat {params.assemblyfiles} > {output}
         '''
-        
\ No newline at end of file
+        
diff --git a/rules/12-MAD.smk b/rules/12-MAD.smk
index 6044d44..1d78396 100644
--- a/rules/12-MAD.smk
+++ b/rules/12-MAD.smk
@@ -116,7 +116,7 @@ rule replace_mad_ids:
                                  "rename","MAD.{filter_workflow}.fasta")
     run:
         sequences=[curr for curr in SeqIO.parse(input.mad,"fasta")]
-        concordance=pd.read_csv(input.concordance,sep="\s+")
+        concordance=pd.read_csv(input.concordance,sep="\\s+")
         concord_dict=dict(zip(concordance["MAD_id"],concordance["Concordance_Short_ID"]))
         for i,curr in enumerate(sequences):
             curr.id = concord_dict[curr.id]