Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

          Comment


          • #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...

            Comment


            • #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.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-27-2024, 06:37 PM
              0 responses
              12 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-27-2024, 06:07 PM
              0 responses
              11 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              52 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X