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shapfiles imported by modelbuilder

dear all,

i have a problem with shapefiles imported through model builder.after using model builder most of the junction is disconnected to pipes also some lines is dissconnected from main lines.you know this need great effort so that i can reach to a model which can be run on watergems.

this happens although the files appear to be connected in arcmap.

i  dont know why?

also, i need to know what are the advantage of using geometric networks or feature geodatabase options that appear in modelbuilder for users working under arcmap?