Thank you dezsoe. It worked for X and Z axis. For Y axis, only one of the step motors was moved. I declared step pin as 5 and dir pin as 4. To move both 2 Y axes, what should I do?
It's strange. I checked the M500 profile which is from the Stepcraft installer and it sets only one output pair for Y. Did you change anything in the wiring? Can you upload your Stepcraft_M500.pro?