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From: Adam P. <aph...@gm...> - 2014-07-23 19:51:50
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Hi Astrid, It is most likely a memory issue. How much RAM does your machine have? As a rule of thumb, MUMmer requires approximately 17 bytes per base-pair of reference sequence. For a reference of your size, that would be over 8GB. If it is possible to partition your reference into multiple files, you can run mummer separately on each, which will save memory. No, MUMmer does not currently support multithreading. Best, -Adam On Tue, Jul 22, 2014 at 9:00 AM, astrid boehne <ast...@un...> wrote: > Hi > I am trying to run mummer to compare very similar genome assemblies (two > individuals of the same species) > and get back the following error. > I reduced the query and reference sequence size I used to match the > character limitations. > 1: PREPARING DATA > 2,3: RUNNING mummer AND CREATING CLUSTERS > # reading input file "ref_qry.ntref" of length 497187885 > # construct suffix tree for sequence of length 497187885 > # (maximum reference length is 536870908) > # (maximum query length is 4294967295) > # process 4971878 characters per dot > > #............................................................................ERROR: > mummer and/or mgaps returned non-zero > > Any suggestions on what is happening? > My guess is that this is a memory issue. > Is it possible to run Mummer multi-threaded? > Thank you very much in advance > All the best > Astrid Böhne > > -- > Astrid Böhne > Universität Basel > Zoologisches Institut > Evolutionsbiologie > Vesalgasse 1 > CH-4051 Basel > Switzerland > Phone +41 (0)61 267 03 05 > Fax +41 (0) 61 267 03 01 > > > > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |