Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • elfuser
    Member
    • Dec 2009
    • 16

    #1

    usearch --cluster causes "Segmentation fault (core dumped)"

    I am running USEARCH 5.1.221 in a ubuntu pangolin 64 bit, and I am trying to run the following command, which is part of the otupipe.bash,

    Code:
    usearch --cluster temp/derep.fas --consout temp/cons.fa --id 0.97 --log temp/cluster_err.log --w 20 --slots 16769023 --maxrejects 64 --sizein --sizeout --usersort
    And I get

    Code:
    3517 Segmentation fault      (core dumped)
    I run any other option in usearch and it works fine, please help
  • me_myself_andI
    Member
    • Nov 2010
    • 30

    #2
    Just a guess: you might be running out of memory. If that is the case, you might want to try --mergesort, but I'm not sure if this works in conjunction with --usersort.

    Andreas

    Comment

    Latest Articles

    Collapse

    • SEQadmin2
      Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
      by SEQadmin2



      CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

      Despite this, “CRISPR helped turn genome editing from a specialized technique into
      ...
      07-31-2026, 11:01 AM
    • SEQadmin2
      Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
      by SEQadmin2


      Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

      The systematic characterization of the human proteome has
      ...
      07-20-2026, 11:48 AM
    • SEQadmin2
      Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
      by SEQadmin2



      Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
      ...
      07-09-2026, 11:10 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, Yesterday, 10:13 AM
    0 responses
    14 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 07-31-2026, 02:55 AM
    0 responses
    29 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 07-24-2026, 12:17 PM
    0 responses
    23 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 07-23-2026, 11:41 AM
    0 responses
    21 views
    0 reactions
    Last Post SEQadmin2  
    Working...