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  • STAR core dump

    I havent been able to run STAR successfully yet. It exits with a core dump message. Any clues?



    Aug 29 20:52:35 ..... Started STAR run
    Aug 29 20:52:35 ... Starting to generate Genome files

    terminate called after throwing an instance of 'std::bad_alloc'
    what(): std::bad_alloc

  • #2
    What OS is this? Did you compile STAR on this machine or download the binaries?

    Comment


    • #3
      In addition to what GenoMax wrote, how much RAM does the computer you're using have?

      Comment


      • #4
        I compiled the libraries myself

        I have about 0.5G of RAM, however have about 12G of swap virtual memory.

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        • #5
          That's unlikely to be enough, unless you work on bacteria or something like that. You'll need to use a bigger computer.

          Comment


          • #6
            Defining large amounts of swap does not help with lack of real memory. I concur with Devon about finding alternate hardware.

            If you are working with NGS data then 512 MB of RAM (I really hope 0.5G is a typo) is not going to get you anywhere with any program.

            STAR major memory requirements posted by Alex in a thread on STAR on the google group:
            1. Genome + SA: ~9*GenomeLength bytes
            2. SAindex: ~6*4^(--genomeSAindexNbases). By default --genomeSAindexNbases 14 and it takes 1.5GB of RAM.
            Last edited by GenoMax; 08-30-2013, 02:19 PM.

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            • #7
              With so little RAM, it doesn't make sense to use rna-star

              Comment

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