The flatten_roda.sh has problems.

[smallfishabc]

1.There is a missing space on line 32.
2.subdir is a relative path, not an absolute path. Therefore, according to the tutorial, it will not work. ChatGPT helped me fix this, and I will paste the corrected script here.
3.It takes 5-6 hours for a data transfer node on a cluster with 2 x 100G ethernet connections to download the alignment files. The flatten_roda.sh script chooses to use mv and rm to move and remove files. If anything happens during this process, users will need to redownload the data.
4.There is no output to track the progress.

for chain_dir in $(ls "${RODA_DIR}"); do
    CHAIN_DIR_PATH="${RODA_DIR}/${chain_dir}"
    for subdir in $(ls "${CHAIN_DIR_PATH}"); do
        SUBDIR_PATH="${CHAIN_DIR_PATH}/${subdir}"
        if [[ ! -d "$SUBDIR_PATH" ]]; then
            echo "$SUBDIR_PATH is not directory"
            continue
        elif [[ -z $(ls "${SUBDIR_PATH}") ]]; then
            continue
        elif [[ $subdir = "pdb" ]] || [[ $subdir = "cif" ]]; then
            cp -r "${SUBDIR_PATH}/"/* "${DATA_DIR}"
        else
            CHAIN_ALIGNMENT_DIR="${ALIGNMENT_DIR}/${chain_dir}"
            mkdir -p "${CHAIN_ALIGNMENT_DIR}"
            cp -r "${SUBDIR_PATH}"/* "${CHAIN_ALIGNMENT_DIR}"
        fi
    done
done