Following methods can help to access the assembly correctness:
Remove the contaminated reads, map the it. If many reads didn't aligned you probably miss some regions in your assembly.
Use a reference genome, and if there are more than 2/MY...
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.
Detail paper...