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  • Bfast

    Can you help me?
    I have read the paper about BFAST, but I am sure I can't index well. My data is about large genome (~2.7Gbp), and the source is mate-pair SOLID reads(length:50bp). I have created a reference genome in nt and another in cs. Now, I run command: bfast index -f hg19.fa -A 1 -m 111111111111111111 -w 18 -n 8
    another one: bfast index -f hg19.fa -A 1 -m 1111110011111110011111 -w 18 -n 8
    I got the under warnings from both them:
    Sorting by thread...
    ^M^H100.000 percent complete^Mthread 100.000 percent complete^MWaiting for other threads to complete...^MMerging sorts from threads...
    Out of 3 required merges, currently on:
    0^M1^M2^M3
    Merge complete.
    Sorted.
    ************************************************************
    ^MIn function "RGIndexCreateHash": Fatal Error[MallocMemory]. Variable/Value: index->starts.
    Message: Could not allocate memory.
    ***** Exiting due to errors *****
    ************************************************************
    Can anyone give me some suggestions about bfast index? I feel so hard to get it clean in my main. THank you!

  • #2
    Originally posted by Lv Ray View Post
    Message: Could not allocate memory.
    Looks like you don't have or you don't provide enough memory for the program.

    Comment


    • #3
      Originally posted by WhatsOEver View Post
      Looks like you don't have or you don't provide enough memory for the program.
      But I have about 300G RAM.

      Comment


      • #4
        cross posted on biostars: https://www.biostars.org/p/112402/

        Comment


        • #5
          Originally posted by lindenb View Post
          cross posted on biostars: https://www.biostars.org/p/112402/
          I am so sorry for my hasty, but I will be mad for bfast index. Sorry for the cross posts.

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          • #6
            I would strongly recommend NovoalignCS for Solid data. I know it's commercial, but it's quite cheap and they do have a trial available. Otherwise algorithms for Solid data are fairly limited - and yes, we did test them all...

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            • #7
              Originally posted by colindaven View Post
              I would strongly recommend NovoalignCS for Solid data. I know it's commercial, but it's quite cheap and they do have a trial available. Otherwise algorithms for Solid data are fairly limited - and yes, we did test them all...
              Thank you. I will use the bfast after my groping it for several days.Maybe I will use NovoalignCS as your said while the bfast is hard to align more reads on ref.
              Thank you again.

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