Using MUMmer 3.9.4
I am trying to install MUMmer 3.9.4 on Ubuntu, following the instructions given here:
When I try to run nucmer, I get this error message:
nucmer: error while loading shared libraries: libumdmummer.so.0:
cannot open shared object file: No such file or directory
I have tried to look it up online, but can't seem to find anything.
Any help would be greatly appreciated!
I had the same problem as you, I did these steps and it helped:
This is critical: Uninstall the existing MUMmer with Synaptic Package Manager. (If you install with
sudo apt-get install mummeryou get v 3.22 and it is still called by any software which you use. This is why you cannot use the option
CPPFLAGS="-O3 -DSIXTYFOURBITS" to install 64-bit Mummer). Download the stable MUMer distro 3.23 from
https://github.com/gmarcais/mummer Extract the package
Install MUMer with this code:
make install CPPFLAGS="-O3 -DSIXTYFOURBITS"
In the end you will get:
(maximum reference length is 2305843009213693948)
(maximum query length is 18446744073709551615)
process 6420479 characters per dot
My OS Ubuntu 14, 64 bit.
Hope it helps.
Actually an update, I somehow got over the libumdmummer.so.0 issue, but somehow I see that the size limit still has not changed.
The genomes that I am trying to align on about 1GB each. Should I use MUMmer? I seem to read in other threads that MUMmer can be very memory-intensive if the files are large.
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