diff --git a/scripts/download_mgnify.sh b/scripts/download_mgnify.sh
index 04f552c4b..f70a54d8f 100755
--- a/scripts/download_mgnify.sh
+++ b/scripts/download_mgnify.sh
@@ -39,5 +39,5 @@ BASENAME=$(basename "${SOURCE_URL}")
 mkdir --parents "${ROOT_DIR}"
 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
-gunzip "${ROOT_DIR}/${BASENAME}"
+gunzip "${BASENAME}"
 popd
diff --git a/scripts/download_small_bfd.sh b/scripts/download_small_bfd.sh
index 0b775fa4e..640e32976 100755
--- a/scripts/download_small_bfd.sh
+++ b/scripts/download_small_bfd.sh
@@ -37,5 +37,5 @@ BASENAME=$(basename "${SOURCE_URL}")
 mkdir --parents "${ROOT_DIR}"
 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
-gunzip "${ROOT_DIR}/${BASENAME}"
+gunzip "${BASENAME}"
 popd
diff --git a/scripts/download_uniprot.sh b/scripts/download_uniprot.sh
index e815e3c3f..d36bb3918 100755
--- a/scripts/download_uniprot.sh
+++ b/scripts/download_uniprot.sh
@@ -45,11 +45,11 @@ mkdir --parents "${ROOT_DIR}"
 aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
 aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
-gunzip "${ROOT_DIR}/${TREMBL_BASENAME}"
-gunzip "${ROOT_DIR}/${SPROT_BASENAME}"
+gunzip "${TREMBL_BASENAME}"
+gunzip "${SPROT_BASENAME}"
 
 # Concatenate TrEMBL and SwissProt, rename to uniprot and clean up.
-cat "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}" >> "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}"
-mv "${ROOT_DIR}/${TREMBL_UNZIPPED_BASENAME}" "${ROOT_DIR}/uniprot.fasta"
-rm "${ROOT_DIR}/${SPROT_UNZIPPED_BASENAME}"
+cat "${SPROT_UNZIPPED_BASENAME}" >> "${TREMBL_UNZIPPED_BASENAME}"
+mv "${TREMBL_UNZIPPED_BASENAME}" "uniprot.fasta"
+rm "${SPROT_UNZIPPED_BASENAME}"
 popd
diff --git a/scripts/download_uniref90.sh b/scripts/download_uniref90.sh
index 27e48883e..4a60d3163 100755
--- a/scripts/download_uniref90.sh
+++ b/scripts/download_uniref90.sh
@@ -37,5 +37,5 @@ BASENAME=$(basename "${SOURCE_URL}")
 mkdir --parents "${ROOT_DIR}"
 aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
-gunzip "${ROOT_DIR}/${BASENAME}"
+gunzip "${BASENAME}"
 popd