Because that version of MUMmer has a query size limit, and my genome files are twice the size of that. I have tried the make CPPFLAGS="-O3 -DSIXTYFOURBITS" get-around, but it doesn't work.
The 3.9.4 version says that it increased the size limit to 120TB, so I wanted to see if this works.
@nancydong20
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).
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.
1GB genomes should fit into (signed) 32-bit integers. Depending on how MUMmer handles the reverse complement, deactivating that, might give you an extra spare bit.
IIRC, Mummer uses ~7 byte per input nucleotide for the suffix tree. That should give you an estimate of how much memory you will need.
Why don't you just install the package?
sudo apt-get install mummerBecause that version of MUMmer has a query size limit, and my genome files are twice the size of that. I have tried the make CPPFLAGS="-O3 -DSIXTYFOURBITS" get-around, but it doesn't work.
The 3.9.4 version says that it increased the size limit to 120TB, so I wanted to see if this works.