when i use \setbeamercovered{invisible} the footline disappear in the whole tikzpicture frames:
\documentclass{beamer}
\usetheme{warsaw}
\usepackage{tikz}
\usetikzlibrary{shapes.geometric, arrows}
\usetikzlibrary{positioning}
\begin{document}
\begin{frame}{frame}
\setbeamercovered{invisible}%transparent=0}
\centering
\begin{tikzpicture}[node distance=.5cm, auto]
\tikzset{
mynode/.style={rectangle,rounded corners,draw=black, top color=green, bottom color=red!80,very thick, inner sep=1em, minimum size=3em, text centered},
myarrow/.style={->, >=latex', shorten >=.1pt},%, thick
mylabel/.style={text width=7em, text centered}
}
\node [mynode](node) {1};\pause
\node [below=of node,mynode](node1){2};
\draw [myarrow] (node.south) -- ++(0,0) -- ++(0,-.2) -| (node1.north);\pause
\node [left=of node1,mynode](node2){2};
\draw [myarrow] (node.south) -- ++(0,0) -- ++(0,-.2) -| (node2.north);\pause
\node [left=of node2,mynode](node3){4};
\draw[myarrow] (node.south) -- ++(0,0) -- ++(0,-.2) -| (node3.north);\pause
\node [right=of node1,mynode](node4){5};
\draw[myarrow] (node.south) -- ++(0,0) -- ++(0,-.2) -| (node4.north);\pause
\node [right=of node4,mynode](node5){6};
\draw[myarrow] (node.south) -- ++(0,0) -- ++(0,-.2) -| (node5.north);
\end{tikzpicture}
\end{frame}
\end{document}

transparent=0, which does print the nodes on the slide (they are selectable with the mouse etc.) but they appear the same as when usinginvisible, i.e., you don't see them. – Marijn Apr 15 '19 at 11:03transparent=0(and no footlines except for the last page withinvisible). Maybe you have a different version ofbeamer? In any case it is just a workaround, it does not solve the actual problem but you can use it as a non-perfect solution in case you don't find the 'real' solution. – Marijn Apr 15 '19 at 11:46node, start drawing halfway down the arrow for the remaining nodes with\usetikzlibrary{calc}and\draw [myarrow] ($(node.south)+(-0.008,-0.2)$) -| (node2.north);\pause. But it is getting increasingly more desirable to solve the original problem :) – Marijn Apr 15 '19 at 12:25