While streaming in the gds file (generated by innovus), I am not able to see all the layers even the metal connection are missing only the drawing of outline are present.
check the GDSII file using a simple visualizer like Klayout or calibredrv.
If the layers are there, the problem is in streaming it it. Check the logs. I assume you are using Virtuoso for stream in, if it encounters problems it usually issues warning but does not stop. So check the logs.
If the layers are not there, the problem is in streaming it out from Innovus. Check your layer map file and the logs.