The runCA parameter utgErrorLimit=2.5 is recommended for Illumina data. It would be nice is that were the default behavior when Illumina data is present.
Here is a suggested implementation. The fastqToCA utility could generate a flag if the reads were short. It would add the flag to the LIB message in the FRG file. The flag would say that reads in this library should be tested by the number-of-errors model. The gatekeeper would store the flag in the gkpStore. When runCA calls BOG, it would test whether the majority of reads belong to libraries with that flag. If so, it would call BOG with utgErrorLimit=2.5. Of course, if the user spec file had set utgErrorLimit to any value, including zero, then the user setting would override this default behavior.