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  • RyNkA
    Member
    • Jul 2013
    • 20
    #1

    oases memory

    I was trying to run velvet/oases with kmer from 25 toward 67 on my local HPC, setting it to run with 256GB of ram. Velveth/g performed well, while oases stopped after around 10 hrs and displayed an error.

    job killed: mem 269731380kb exceeded limit 268435456kb

    My command was oases transcripts_69 -min_trans_lgth 200...Any suggestion ?
    Tags: None
  • shunyip
    Member
    • Oct 2013
    • 20
    #2
    Many HPCs have a setting that limits the maximum amount of ram that you can use in a job. If your job exceed that amount, it will be killed. In this case, it is 268435456kb.

    It appears that this oases job requires more ram than your HPC allows. You should contact your HPC's administrator to see if you can gain access to more ram for this job; or you can find a way to decrease ram usage.

    Comment

    • RyNkA
      Member
      • Jul 2013
      • 20
      #3
      Originally posted by shunyip View Post
      Many HPCs have a setting that limits the maximum amount of ram that you can use in a job. If your job exceed that amount, it will be killed. In this case, it is 268435456kb.

      It appears that this oases job requires more ram than your HPC allows. You should contact your HPC's administrator to see if you can gain access to more ram for this job; or you can find a way to decrease ram usage.
      Yes, I'm pretty well aware that Oases did actually exceed the amount of RAM allocated by the HPC. However i would like to ask if there is anyway to decrease ram usage. I've dig some search and they suggest that I lower the kmer value (which i did manage to do it at 31 kmer, however, the problem still presists)

      Cheers,

      Comment

      • shunyip
        Member
        • Oct 2013
        • 20
        #4
        At the FAQ section of Oases' manual, they suggested several more ways for you to decrease the memory usage also.
        Error: 500
        http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf


        Hopefully it helps,

        Comment

        • jgibbons1
          Senior Member
          • Oct 2009
          • 135
          #5
          Originally posted by RyNkA View Post
          I was trying to run velvet/oases with kmer from 25 toward 67 on my local HPC, setting it to run with 256GB of ram. Velveth/g performed well, while oases stopped after around 10 hrs and displayed an error.

          job killed: mem 269731380kb exceeded limit 268435456kb

          My command was oases transcripts_69 -min_trans_lgth 200...Any suggestion ?
          Just out of curiosity, how many reads are you trying to assemble? Paired end or single end? Have you quality trimmed your data before assembling?

          Comment

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