diff --git a/freyja/_cli.py b/freyja/_cli.py
index 9f7a6b41..39020a42 100644
--- a/freyja/_cli.py
+++ b/freyja/_cli.py
@@ -64,7 +64,9 @@ def update():
     df_barcodes = convert_to_barcodes(df)
     df_barcodes = reversion_checking(df_barcodes)
     df_barcodes.to_csv(os.path.join(locDir, 'data/usher_barcodes.csv'))
-    # TODO: delete files generated along the way
+    # delete files generated along the way that aren't needed anymore
+    os.remove(lineagePath)
+    os.remove(os.path.join(locDir, "data/public-latest.all.masked.pb.gz"))
 
 
 @cli.command()
diff --git a/freyja/sample_deconv.py b/freyja/sample_deconv.py
index f1094e31..f432433c 100644
--- a/freyja/sample_deconv.py
+++ b/freyja/sample_deconv.py
@@ -41,7 +41,7 @@ def build_mix_and_depth_arrays(fn, depthFn, muts):
 
 def reindex_dfs(df_barcodes, mix, depths):
     # first, drop Nextstrain clade names.
-    nxNames = ['20A', '20C', '20D', '20H(Beta,V2)', '21C(Epsilon)']
+    nxNames = df_barcodes.index[df_barcodes.index.str[0].str.isdigit()]
     dropList = set(nxNames) & set(df_barcodes.index)
     df_barcodes = df_barcodes.drop(index=dropList)
     # reindex everything to match across the dfs
diff --git a/freyja/updates.py b/freyja/updates.py
index f7b80326..4a6be100 100644
--- a/freyja/updates.py
+++ b/freyja/updates.py
@@ -13,7 +13,6 @@ def download_tree():
 
 
 def convert_tree():
-    print('Converting tree into barcodes',)
     locDir = os.path.abspath(os.path.join(os.path.realpath(__file__),
                                           os.pardir))
     treePath = os.path.join(locDir, "data/public-latest.all.masked.pb.gz")
@@ -25,7 +24,6 @@ def convert_tree():
 def get_curated_lineage_data():
     locDir = os.path.abspath(os.path.join(os.path.realpath(__file__),
                                           os.pardir))
-    print('Downloading an updated curated lineage set from outbreak.info')
     url2 = "https://raw.githubusercontent.com/outbreak-info/outbreak.info/"\
            "master/web/src/assets/genomics/curated_lineages.json"
     urllib.request.urlretrieve(url2,
diff --git a/preprocess.sh b/preprocess.sh
deleted file mode 100644
index 72e3dc00..00000000
--- a/preprocess.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-bamfolder=$1
-varfolder=$2
-depthfolder=$3
-# echo "${depthfolder}"
-if [[ $# -eq 0 ]] ; then
-    echo 'Need to supply input arguments.'
-    exit 1
-fi
-
-for fn in $1/* ## bamfiles/* 
-do
-    # echo "${fn}"
-    # echo "${fn%.*}" 
-    # echo "${fn##*/}" 
-    fn_out=${fn##*/}
-    baseName=${fn##*/}
-    baseName=${baseName%.*}
-    echo $depthfolder$baseName
-    samtools mpileup -aa -A -d 600000 -Q 20 -q 0 -B -f NC_045512_Hu-1.fasta ${fn} | tee >(cut -f1-4 > ${depthfolder}${fn_out%.*}.depth) | ivar variants -p $depthfolder$baseName -q 20 -r NC_045512_Hu-1.fasta
-    # samtools mpileup -A -aa -d 600000 -Q 20 -q 0 -B -f NC_045512_Hu-1.fasta ${fn} | cut -f1-4 > ${depthfolder}${fn_out%.*}.depth #&
-done
-
-