search

mummer4 / mummer

Mummer alignment tool
Artistic License 2.0
458 stars 107 forks source link

a problem of the using RAM of this software #47

Open milkcookie opened 6 years ago

milkcookie commented 6 years ago

Dear all： I want to identify variation between two similar genome, but when I use Mummer4 it use almost more than 1000Gb RAM, our linux server can't run with it, the larger one genome size is about 525Mb, the other one is about 350Mb, I want to know how can I limit the RAM when I use this software? whether the software have a limit of genome size? nucmer --maxmatch --prefix=test test1.fasta test2.fasta Thanks FAFU milk

kloetzl commented 6 years ago

You could try the patch from #30. It makes nucmer faster and use significantly less memory.

alienzj commented 6 years ago

!!! 2018-03-12 11:19:17 Doing step 20: Getting overlaps !!! 2018-03-12 11:19:17 Running: nucmer -maxmatch -c 100 292S_more2kb_contigs_nr.ref.seq 292S_more2kb_contigs_nr.qry.seq -p 292S_more2kb_contigs_nr 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS reading input file "292S_more2kb_contigs_nr.ntref" of length 32244835963 construct suffix tree for sequence of length 32244835963 (maximum reference length is 2305843009213693948) (maximum query length is 18446744073709551615) process 322448359 characters per dot file "construct.c", line 878: allocandusespaceviaptr(8,48367253946) failed:not enough memory ERROR: mummer and/or mgaps returned non-zero !!! 2018-03-12 12:11:09 Command: nucmer -maxmatch -c 100 292S_more2kb_contigs_nr.ref.seq 292S_more2kb_contigs_nr.qry.seq -p 292S_more2kb_contigs_nr exited with status: 1 !!! END - Elapsed time: 0d 0h 51m 52s

alienzj commented 6 years ago

Hello, 30 Gb contigs vs 30Gb contigs, how much memory will be used?

milkcookie commented 6 years ago

Hi thanks @kloetzl , sorry to reply later, I hava install the software Tumer, but I don't know how to use it with Mummer. Hi @alienzj ,I think you can split itfor SV detection, its too big for Mummer.

kloetzl commented 6 years ago

30 Gb contigs, how much memory will be used?

IIRC, mummer uses roughly 7byte per input nucleotide.

You might have another problem here: You need more than 32bits to represent the length of the genome. I am not sure if mummer correctly handles lengths with 64bit integers (judging from the line with the error, it doesn't).

Hi thanks @kloetzl, sorry to reply later, I hava install the software Tummer, but I don't know how to use it with Mummer.

TUMmer is just a replacement for the MUMmer executable. So you would call it with the same set of parameters. If you have any specific inquiries, please open an issue in the TUMmer repo.