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  • newbler: out of memory.

    I am getting an out of memory error using newbler 2.8
    #runAssembly 2.8 (20120726_1306)
    I have around 7GB of single end sequencing data from a 65Mb diploid genome. ~16 million reads.
    I have a machine with 62Gb memory, so memory requirements should be well within that.
    newbler complains it is out of memory even though it is using only ~4GB.

    I've seen similar posts, but they just say to rerun, but that does not work for me.

    any help would be appreciated.

    output is below.

    Assembly computation starting at: Wed Apr 24 12:37:57 2013 (v2.8 (20120726_1306))
    Building contigs/scaffolds...
    -> 12731 large contigs, 19863 all contigs
    Computing signals...
    -> 10200000 of 50076485...Reading flowgrams...
    -> 45600000 of 50076485...Reading flowgrams...
    -> 50076485 of 50076485...
    Checkpointing...
    Generating output...
    -> 45600000 of 50076485...Reading flowgrams...
    -> 50000000 of 50076485...
    Error: The computation ran out of memory and is unable to continue.

  • #2
    Are you running into some kind of system resource limit?
    Was newbler compiled on this machine?

    Comment


    • #3
      thanks GenoMax -

      Newbler was not compiled on the machine, and it is a 32bit executable.
      I think that explains the problem.

      I'll get back to Roche to see if they have a 64bit version or can provide the source.

      thanks for the nudge in the right direction.

      Comment


      • #4
        In case someone else finds this useful

        use linux command 'file runAssembly'
        #file ../apps/mapper/bin/runAssembly
        ../apps/mapper/bin/runAssembly: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.3, not stripped

        compare with a 64bit executable of version 2.7
        #file runAssembly
        runAssembly: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.3, not stripped

        the latter version worked with my data.

        Comment

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