There is some issue with the implement script. So I took the manual steps.
1. Created the pcie core using core generator.
2. Implement the core by running the implement.bat in implement folder.
2. Create a new ISE project.
3. Add the DMA refereance design files required. (Either 32 or 64 files)
4. Add the created <pcie_core>.ngc file to the project.
5. Implement the whole design using ISE.
6. It created the bit file and finished successfully.
转载自：http://blog.csdn.net/jasonwoodlee/article/details/6708441