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  • Mira4 Assembler using all memory for denovo, est assembly

    Hi Users,

    My PC has 48 GB of RAM and 8 CPU. I am trying to create denovo assembly using Mira 4 Assembler. Input file has only 2 fastq files with only 30 million reads with sequence length 50-350 nt.

    I used below manifest.comf file

    project = miraproject job = est, denovo, accurate
    parameters = COMMON_SETTINGS -GENERAL:number_of_threads=4 amm=off -HS:mnr=yes:nrr=8
    parameters = IONTOR_SETTINGS -CL:qc=no -ALIGN: min_relative_score=90 -ASSEMBLY:minimum_read_length=200

    readgroup = SomeUnpairedIonTorrentReadsIGotFromTheLab
    technology = iontor
    data = /media/DATAPART3/Combine_Files/miraproject/data/


    But problem is it is taking long time more than 20 hours and it is using all the memory.

    Any suggestion?


    I would really appreciate your help.

    Thanks in advance.
    Naresh

  • #2
    Hi Users,

    bump....

    Comment


    • #3
      You should post the issue on the mira mailing list.

      Comment


      • #4
        You may also consider SPAdes 3.0, which contains experimental IonTorrent error correction and assembly module.

        Comment


        • #5
          SPAdes

          Hi akorobeynikov,

          Thanks for your reply. I am doing transcriptome analysis and SPAdes is useful for only genome analysis.
          Am i right?

          Best,
          Naresh




          Originally posted by akorobeynikov View Post
          You may also consider SPAdes 3.0, which contains experimental IonTorrent error correction and assembly module.

          Comment


          • #6
            Hi sklages,

            I contacted them, they just told me get new computer resources with more GB on it.

            Thanks,
            Naresh


            Originally posted by sklages View Post
            You should post the issue on the mira mailing list.

            Comment


            • #7
              Originally posted by nareshvasani View Post
              Thanks for your reply. I am doing transcriptome analysis and SPAdes is useful for only genome analysis.
              Am i right?
              Well, I never did this by myself, but rumors are that you still
              may try to assemble them in single-cell mode. I'd select the standard set of kmers, that is - 21,33,55

              Comment


              • #8
                Try a less memory-heavy assembler that is based on de bruijn graphs (eg Trinity, transABYSS)? I think Mira is based at least partially on overlap-layout-consensus so will be very memory hungry. If you have 30 million reads, this line from the Mira4 manual may be relevant:

                1.4. For which data sets to use MIRA and for which not

                As a general rule of thumb: if you have an organism with more than 100 to 150 megabases or more than 20 to 40 million reads, you might want to try other assemblers first.

                Comment

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