Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • dmacmillan
    Member
    • Jan 2012
    • 49
    #1

    Oases Help

    I get an error when trying to do the final merge stage of oases. This is my command and output:

    ../assemblers/oases_0.2.07_x11/oases MergedAssembly/ -merge yes

    [0.000000] Reading graph file MergedAssembly//Graph2
    [0.023690] Graph has 2355595 nodes and 5929364 sequences
    [1282.942385] Reading read set file MergedAssembly//Sequences;
    [1293.465792] 5929364 sequences found
    [1327.296416] Done
    [1389.423138] Removing contigs with coverage < 3.000000...
    [1389.502600] Concatenation...
    [1389.918961] Renumbering nodes
    [1389.918980] Initial node count 2355595
    [1389.923377] Removed 0 null nodes
    [1389.923396] Concatenation over!
    [1389.923399] Clipping short tips off graph, drastic
    [1389.970080] Concatenation...
    [1390.386237] Renumbering nodes
    [1390.386257] Initial node count 2355595
    [1390.390656] Removed 0 null nodes
    [1390.390673] Concatenation over!
    [1390.390675] 2355595 nodes left
    [1390.390683] Correcting graph with cutoff 0.200000
    [1390.390691] Removing low coverage edges from the graph
    Segmentation fault

    Has anyone experienced anything such as this? If so do you have any ideas as to how I can get around it?
    Last edited by dmacmillan; 07-03-2012, 09:01 AM.
    Tags: oases velvet
  • robertorun
    Member
    • Nov 2009
    • 22
    #2
    I also met the same errors.
    I only downloaded the lastest velvet and oases , then recompile them , now ,they are work smoothly!

    Comment

    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Nine Things a Sample Prep Scientist Thinks About Before Sequencing
      by SEQadmin2


      I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

      Here are nine questions we think about, in roughly the order they matter, before...
      Today, 07:11 AM
    • SEQadmin2
      From Collection to Sequencing: Why Sample Preparation and Preservation Define Sequencing Data
      by SEQadmin2


      Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.

      The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
      ...
      06-02-2026, 10:05 AM
    • SEQadmin2
      Single-Cell Sequencing at an Inflection Point: Early Impacts of New Platforms and Emerging Trends
      by SEQadmin2


      With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.

      Introduction

      Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...
      05-22-2026, 06:42 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2
    Started by SEQadmin2, Yesterday, 06:09 AM
    0 responses
    16 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 06:09 AM  
    Sequencing the Two-Toed Sloth Genome Reveals Jumping Genes Tied to Its Extreme Metabolism by SEQadmin2
    Started by SEQadmin2, 06-09-2026, 11:58 AM
    0 responses
    37 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-09-2026, 11:58 AM  
    A New Method Makes Hantavirus Genome Analysis Faster and More Accessible by SEQadmin2
    Started by SEQadmin2, 06-05-2026, 10:09 AM
    0 responses
    43 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-05-2026, 10:09 AM  
    A New Single-Cell Method Maps DNA-Protein Interactions by SEQadmin2
    Started by SEQadmin2, 06-04-2026, 08:59 AM
    0 responses
    49 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    06-04-2026, 08:59 AM  
    View All
    Working...