Hi Ryan, The error message you've posted indicates that mauveAligner is running out of memory when trying to complete the alignment. It's difficult to say exactly why that happened without the middle part of the console log (i only see the beginning and end posted with your message). Aligning 30 complete S. cerevisiae genomes will definitely require more than 2GB of RAM with progressiveMauve, and may also require >2GB with mauveAligner. We are working to reduce memory consumption for the next release.
Possibly related to the error message: I notice your sequence data is stored in a single input file named all_genomes.fas. Are the sequences all finished and unichromosomal? If they haven't yet been finished but are in multiple contigs, or there is more than one chromosome being aligned, then it will be necessary to split the input into one file per genome sequence. The underlying reason is that when input is given as a single file, mauveAligner and progressiveMauve treat each sequence entry in the Multi-FastA/GenBank file as coming from a separate organism. Thus, contigs or chromosomes from the same organism would be treated as separate organisms. Hope that helps, -Aaron Ryan Ames wrote: > Hi Everyone > > Sorry for posting what might be an easy problem to the list but I > could really use some help. > > Im trying to use mauve to align >30 genomes and get some alignment > data I could use for phylogenetic analysis. (The alignment obviously > doesn't have to be the whole genomes just a few select Islands would > be good) > However mauve keeps crashing when I try and run it. > > Im using Mac OS X 10.4+ 2.16 GHz Intel Core 2 Duo 2GB 667 MHz DDR2 SDRAM > > my command line input is > /Applications/Mauve.app/Contents/MacOS/mauveAligner --output=/Users/ > home/mauve/all_cerevisiae.mauv --island-size=50 --island-output=/ > Users/hom > e/mauve/all_cerevisiae.mauv.islands --backbone-size=50 --max-backbone- > gap=50 --backbone-output=/Users/home/mauve/all_cerevisiae.mauv.backbone > --id-matrix=/Users/home/mauve/all_cerevisiae.mauv.id_matrix --output- > alignment=/Users/home/mauve/all_cerevisiae.mauv.alignment --output- > guide- > tree=/Users/home/mauve/all_cerevisiae.mauv.guide_tree /Users/home/ > mauve/all_genomes.fas > > The errors Im getting are: > mauveAligner(322) malloc: *** vm_allocate(size=1069056) failed (error > code=3) > Exited with error code: 134 > mauveAligner(322) malloc: *** error: can't allocate region > mauveAligner(322) malloc: *** set a breakpoint in szone_error to debug > mauveAligner(322) malloc: *** vm_allocate(size=1069056) failed (error > code=3) > mauveAligner(322) malloc: *** error: can't allocate region > mauveAligner(322) malloc: *** set a breakpoint in szone_error to debug > mauveAligner(322) malloc: *** vm_allocate(size=1069056) failed (error > code=3) > mauveAligner(322) malloc: *** error: can't allocate region > mauveAligner(322) malloc: *** set a breakpoint in szone_error to debug > mauveAligner(322) malloc: *** vm_allocate(size=1069056) failed (error > code=3) > mauveAligner(322) malloc: *** error: can't allocate region > mauveAligner(322) malloc: *** set a breakpoint in szone_error to debug > terminate called recursively > > Any help or advice for quicker alignment etc would be great > > Thanks > > Ryan > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
