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  • Pindel memory usage 30x whole genome

    How much memory should Pindel be using on a 30x whole genome? With the smallest window size it is using a large amount of memory even when the log says it is processing a window with only 1000 reads.

  • #2
    can you tell me your Pindel version? You could split calculation by 5MB per job. Sometimes there is extreme high coverage at a few small regions. This causes maximum memory usage going high.

    Kai

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    • #3
      The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.

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      • #4
        Originally posted by Nick View Post
        The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.
        Is it possible to send me the log file or console output to my email [email protected]?

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