I encountered the following error when running nucmer (part of the MUMmer package) for a large genome assembly:
mummer: suffix tree construction failed: textlen=727301215 larger than maximal textlen=536870908
It appears that we can work around this problem by compiling a 64-bit version of mummer. There are two ways of doing this:
- Edit the MUMmer3.23/src/kurtz/libbasedir/types.h file. We need to add the following line “#define SIXTYFOURBITS” before the line “#ifdef SIXTYFOURBITS”. Then run make install to compile the package.
- When compiling the package, use the following command:
make CPPFLAGS=”-O3 -DSIXTYFOURBITS”
Either way should work.