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  • #16
    Extracting the files from sff:

    sff_extract -c -l linker.fasta "insert_size:2500,insert_stdev:500" file1.sff file2.sff -o 3kb_norton

    This worked perfect and had given me the fasta, qual and xml..

    Appending shotgun files:

    sff_extract -a shotgun1.sff shotgun2.sff shotgun3.sff -o 3kb_norton

    This also appended the sff's and the sizes of the initial fasta,qual and xml files changed to a much larger size to allocate the shotgun seqs...

    Assembly:

    mira --project=3kb_norton --job=denovo,genome,accurate,454 -SK:mnr=yes:nrr=10 >&3kb_log_assembly.txt

    now this also showed no error.. it started running.. and after a while below the command it said:
    tcmalloc: large alloc 1482399744 bytes == 0*867e000 @

    and below this, after a while it said:
    Aborted

    Comment


    • #17
      The log file at the end showed this :


      Dynamic allocs: 0
      Align allocs: 0
      Out of memory detected, exception message is: std::bad_alloc

      You are running a 32 bit executable. Please note that the maximum
      theoretical memory a 32 bit programm can use (be it in Linux, Windows or
      other) is 4 GiB, in practice less: between 2.7 and 3.3 GiB. This is valid
      even if your machine has hundreds of GiB.
      Should your machine have more that 4 GiB, use a 64 bit OS and a 64 bit
      version of MIRA.


      ----

      So i downloaded the 64 bit of MIRA and after the command
      mira --project=3kb_norton --job=denovo,genome,accurate,454 -SK:mnr=yes:nrr=10 >&3kb_log_assembly.txt

      it said:
      tcmalloc: large alloc 2323759104 bytes == 0*1f5b9000 @

      so the number of bytes increased

      Comment


      • #18
        It looks like you don't have enough memory to do this assembly. As mentioned before, try the miramem command to estimate the memory requirement for this assembly....that way you'll know if you're in the ball park of what is required by MIRA.
        Last edited by nathanhaigh; 08-17-2011, 04:48 PM. Reason: typo

        Comment


        • #19
          yes seems like it..
          So i just wanted to ask you if appending the shotgun files is a must ?

          have you done the appending and performed the assembly ?

          If NO, what are the softwares u suggest I do a 454 denovo with ?
          Since you converted to fastq, i assume you used an illumina assembler ?

          Comment

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