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  • eseq_prak
    Junior Member
    • Jan 2013
    • 2

    Bwa Index error=12

    Hello,
    Im having an index error as well. I am trying to index human genome build 37. I am using bwa 0.6.2 on a Mac OS 10.5.8, 64 bit, 8GB of RAM and 280GB of space.
    When I run the command:
    bwa index -a bwtsw -p human_g1k_v37 human_g1k_v37.fasta

    BWA starts indexing the genome but stops and provides an error message (error code=12)

    BWTIncConstructFromPacked] 630 iterations done. 1740074246 characters processed.
    [BWTIncConstructFromPacked] 640 iterations done. 1778041526 characters processed.
    [BWTIncConstructFromPacked] 650 iterations done. 1811782918 characters processed.
    [BWTIncConstructFromPacked] 660 iterations done. 1841768294 characters processed.
    [BWTIncConstructFromPacked] 670 iterations done. 1868415350 characters processed.
    [BWTIncConstructFromPacked] 680 iterations done. 1892095270 characters processed.
    [bwt_gen] Finished constructing BWT in 688 iterations.
    [bwa_index] 2010.81 seconds elapse.
    [bwa_index] Update BWT... bwa(3627) malloc: *** mmap(size=3101806592) failed (error code=12)
    *** error: can't allocate region
    *** set a breakpoint in malloc_error_break to debug
    Bus error

    Any Help with this will be appreciated.

    Thanks a bunch!

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