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memory used by DepthOfCoverage


I tried to use DepthOfCoverage to figure out the coverage of 50 whole exome sequencing data. It works fine for single sample, however, the program always complained about memory issue, even I provide 100 GB as "-Xmx100g". Any suggestions for the problem? There is a option "--read_buffer_size", which seems to be helpful, how should set the value ?


Best Answer


  • chunxuanchunxuan Member
    edited March 2014

    Some updates:

    The error output is

    OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x00007ff011600000, 2365587456, 0) failed; error='Cannot allocate memory' (errno=12)

    There is insufficient memory for the Java Runtime Environment to continue.
    Native memory allocation (malloc) failed to allocate 2365587456 bytes for committing reserved memory.

    java -version

    java version "1.6.0_26"

    Java(TM) SE Runtime Environment (build 1.6.0_26-b03)

    Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode)

    Does anyone have similar problem?

  • @Geraldine_VdAuwera said:
    Hi chunxuan,

    DepthOfCoverage is very greedy for memory so running on 50 samples may be an issue, especially if you have areas of very high depth. Unfortunately there's nothing much we can do about that; the recommended way to deal with this is to run DoC separately on each individual sample and then analyze the results jointly using your preferred statistical package.

    A little bit update, do not assign too much memory by -Xmx, some times it will cause the memory issue.

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