diff --git a/README.md b/README.md
index 114d5df1c63541912aa0a8342ffa69ae3d102cbf..a8f6acd400f92f9904846e2e0838acb795448409 100644
--- a/README.md
+++ b/README.md
@@ -20,3 +20,5 @@ The only other file you need to install is `xlsx2csv` using `pip`:
 ```
 pip install xlsx2csv
 ```
+
+Additionally, I used `ripgrep` instead of `grep` for faster extraction of subset data from EggNOG. In case you rely on `grep` make edits accordingly in the notebooks (replace commands of `rg`)
diff --git a/notebooks/01-01_download_data.ipynb b/notebooks/01-01_download_data.ipynb
index 265a7254d60b086f1526bb51770b814e93bc5431..9e6f784243ebbea1e3e2f7d9eb0aff7b9821b32b 100644
--- a/notebooks/01-01_download_data.ipynb
+++ b/notebooks/01-01_download_data.ipynb
@@ -9,8 +9,10 @@
    ]
   },
   {
-   "cell_type": "raw",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
     "e6_url = \"http://eggnog6.embl.de/download/eggnog_6.0/\"\n",
     "all_trees_path = e6_url + \"e6.all_raw_trees_and_algs.tsv\"\n",
@@ -38,12 +40,10 @@
    ]
   },
   {
-   "cell_type": "raw",
-   "metadata": {
-    "vscode": {
-     "languageId": "raw"
-    }
-   },
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "%%bash -s \"$data_dir\" \"$all_trees_path\" \"$og2seqs_species_path\" \"$seq2ogs_path\" \"$gold_url\"\n",
     "pip install xlsx2csv\n",