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  • BFAST Alignment Troubleshoot

    Hi

    I am trying to perform an alignment in colored space with SOLID and I get this error


    In function "RGMatchesRead": Fatal Error[MallocMemory]. Variable/Value: m->ends.
    Message: Could not allocate memory.
    ***** Exiting due to errors *****


    Here is the code I used

    /usr/local/bfast/0.6.5a/bin/bfast localalign -f c_elegans.WS214.dna.fa -A 1 -m c_elegans.WS214.dna.fa.cs.1.1.bif


    Does anyone have any thoughts or helpful tips? Thanks

  • #2
    That looks like it cannot allocate enough memory - how much RAM do you have on your machine?

    Comment


    • #3
      3 GB.

      This should be sufficient, right?

      Comment


      • #4
        Not necessarily, it seems that BFAST it quite RAM hungry, needing about 17-24 GB RAM for an index of the human genome (according to the paper).
        You might want to try bowtie or some other low-mem aligner...

        Comment

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