A reference genome is needed when using cgatools on Complete Genomics data. Here are links to the ftp sites that contain the reference compact randomly accessible reference (.crr) files. Just use the wget command from a UNIX cluster to download.
NCBI Build 36:
NCBI Build 37:
The next step is to verify that the file downloaded completely. Run one of the following commands at the command prompt depending on the version of the .crr file you downloaded.
The file output should look like this for build 36.
And this for build 37.
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