Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Newbler 2.3 on Ubuntu- Anyone?

    I'm running Newbler 2.3 on an Ubuntu box (MacPro, dual quad core, 32 Gb RAM) and having some issues. Wondering if anyone out there is using Ubuntu and experiencing similar problems?

    Everything appears to be working w.r.t. the GUI and the app., especially if I run in genome assembly mode as a complex genome, which seems to work fine. However, when I try to run in cDNA mode (I'm doing de novo transcriptome assembly) it takes forever on even relatively small jobs (2-3 gig 454 data). The exact same data run on a RedHat install takes ~30 min.

    If I try to do a hybrid assembly with ca. 5xe6 seqs (12 gB data), it always stalls during detangling, ~ 55% complete), loses contact with the GUI, and locks one of my cores @ 100% and my RAM @ ~ 14 Gb. I can exit the app., but I have to reboot to free up the core and the RAM.

    Any thoughts/suggestions as to why the cDNA algorithm won't run properly on an Ubuntu install? Roche tech support is working with me, but so far no fixes.

  • #2
    Hello,

    I*am experiencing the exact same problem (cDNA, also MacPro, dual quad core, 32 Gb RAM on ubuntu). I did not have the problem with newbler 2.3.

    The only difference is that the behaviour similar in Red Hat.

    Did you find any reason?

    Best,

    Yvan

    Comment


    • #3
      Yvan,

      Wish I had some good info for you. I'm still running Ver 2.3. My fix was to filter the data outside of Newbler and then do hybrid assemblies using fasta/qual data. Prior to that, I was loading .sff files for the 454 data and fasta/qual files for the Sanger data plus loading my sequencing filtering file for ribosomal, mito, etc...

      Using sff_extract on the 454 data and then filtering all data using a SeqClean pipeline prior to running Newbler (and also without running a filtering file) sped things up significantly and prevented the problems I was experiencing.

      So, I'm not really sure which change helped the most: filtering prior to assembly or assembling only fasta/qual data.

      I'd be interested to know if you discovery anything further.

      Walt

      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, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X