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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:

  1. 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.
  2. When compiling the package, use the following command:
    make clean
    make CPPFLAGS=”-O3 -DSIXTYFOURBITS”

Either way should work.

References

http://seqanswers.com/wiki/Talk:MUMmer
https://sourceforge.net/p/mummer/discussion/451664/thread/59ad55aa/

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