Question: Using MUMmer 3.9.4
1
gravatar for nancydong20
9 months ago by
nancydong2060
nancydong2060 wrote:

Hello everyone!

I am trying to install MUMmer 3.9.4 on Ubuntu, following the instructions given here: https://github.com/gmarcais/mummer/blob/master/INSTALL.md

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!

Nancy

mummer software error • 545 views
ADD COMMENTlink modified 4 days ago by Biostar ♦♦ 20 • written 9 months ago by nancydong2060

Why don't you just install the package? sudo apt-get install mummer

ADD REPLYlink written 9 months ago by kloetzl710

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.

ADD REPLYlink written 9 months ago by nancydong2060
4
gravatar for Bartosz Ulaszewski
9 months ago by
Poland
Bartosz Ulaszewski50 wrote:

@nancydong20 I had the same problem as you, I did these steps and it helped:

  1. 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).
  2. Download the stable MUMer distro 3.23 from https://github.com/gmarcais/mummer
  3. Extract the package
  4. Install MUMer with this code:
  5. cd MUMmer3.23
  6. mkdir aux_bin
  7. make check
  8. make install CPPFLAGS="-O3 -DSIXTYFOURBITS"
  9. mummerpath=pwd
  10. cd ..
  11. export PATH=$mergerpath:$mummerpath:$PATH

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.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Bartosz Ulaszewski50
1

And one more thing in step 9 pwd should be between this symbol `

ADD REPLYlink written 9 months ago by Bartosz Ulaszewski50
1

Thank you SOOO much! It worked!

ADD REPLYlink written 9 months ago by nancydong2060
0
gravatar for nancydong20
9 months ago by
nancydong2060
nancydong2060 wrote:

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.

ADD COMMENTlink modified 9 months ago • written 9 months ago by nancydong2060

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.

ADD REPLYlink written 9 months ago by kloetzl710
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