"Read" command in bash script is being skipped

I'm creating a script to update my linux distribution if I need to wipe the HD or I need to install Linux on another machine. So this script basically install all the programs I usually need. At the beginning a have a "read" command that asks if I want to install all the packages automatically or not. If I choose not, for each program not found it should ask me I want it to be installed and I use this code

if [[ $installall == "yes" ]]; then
    echo " Installing $sciprog..."
    sudo apt-get install -y $sciprog >/dev/null
    {
        scitest=`dpkg -s $sciprog | grep Status`
    } 2>${HOME}/musthave.errorlog
    if [[ $scitest != "Status: install ok installed" ]]; then
        echo " I've encountered problems installing $sciprog that I can't resolve. "
        echo " Consider installing $sciprog manually. "
        {
            echo "=========="
            echo " $sciprog"
        } >>${HOME}/musthave.notinstalled
    else
        echo " $sciprog installed correctly!"
        {
            echo "=========="
            echo " $sciprog"
        } >>${HOME}/musthave.installed
    fi
else
    echo " Seems like $sciprog is not installed... Do you want to download it?"
    echo " Type 'y' for yes."

    read secondyn ### THIS IS THE GUILTY COMMAND ###

    if [[ $secondyn == "y" ]]; then
        echo " Installing $sciprog ..."
        sudo apt-get install -y $sciprog >/dev/null
        {
            checkinstall=`dpkg -s $sciprog | grep Status`
        } 2>>${HOME}/musthave.errorlog
        if [[ $checkinstall != "Status: install ok installed" ]]; then
            echo " I've encountered problems installing $sciprog that I can't resolve. "
            echo " Consider installing $sciprog manually. "
            {
                echo "=========="
                echo " $sciprog"
            } >>${HOME}/musthave.notinstalled
        else
            echo " $sciprog installed correctly!"
            {
                echo "=========="
                echo " $sciprog"
            } >>${HOME}/musthave.installed
        fi
    else
        echo " Skipping $sciprog ..."
        {
            echo "=========="
            echo " $sciprog"
        } >>${HOME}/musthave.notinstalled
    fi
### some more code which works as expected. All the code above is inside a 
### while...do...done loop which reads line by line the file at the end
done <${HOME}/file.list

But if I run the script, it skips the "read" command in the else clause and assumes it to be "n"...

I can't figure out why, there are other read function also inside if...then...else...fi loops and they work as expected...

Any ideas?