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  • #16
    I am running the script on cluster itself. It has 1TB Ram and 64 cores of which 58 are provided for masurca to run.
    How to restart from step "Creating k-unitigs with k=70" ? I am not sure how to do that.

    Thanks.

    Comment


    • #17
      Still you need to check how much RAM your 58 threads consume on your machine.
      Check if IO bandwidth is sufficient; are you the only one reading from / writing to the filesystem with your job?

      Restarting is described in http://www.genome.umd.edu/docs/MaSuR...StartGuide.pdf -- "Restarting failed assembly".

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      • #18
        Yes, I am the only one reading from / writing to the file system with this job. I have re-ran the assembly with Creating k-unitigs with k=70 step. Lets see.

        Thanks.

        Comment


        • #19
          Hi sklages,

          Is there any parameter to define how much memory the process can take or how much memory we want to allot for Masurca? Since I think as you mentioned before also, the error is regarding memory.

          Thanks.

          Comment

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