Using MUMmer 3.9.4
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5.2 years ago
nancydong20 ▴ 110

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 • 4.0k views
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Why don't you just install the package? sudo apt-get install mummer

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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.

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5.2 years ago

@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).
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.

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

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Thank you SOOO much! It worked!

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5.2 years ago
nancydong20 ▴ 110

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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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.