Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Error: Running pindel on breakdancer output

    Hi All,

    I am running breakdancer output in pindel and getting errors. My command is as follows:

    pindel -f human_g1k_v37.fasta -i Sample.config.txt -o Sample.chr11 -c 11 -b Sample.ctx

    I am getting the following errors which produces empty pindel SV files:
    .............................................................................
    Looking at chromosome 11 bases 0 to 5000000.
    [bam_index_load] wrong magic number.
    *** glibc detected *** pindel: double free or corruption (!prev): 0x000000001ef65800 ***
    ..............................................................................
    This is followed by something like "Backtrace" and "Memory map"

    I am using 0.2.4x of May 8, 2013

    Can anyone please tell me what seems to be the problem? I looked around and it looks like no one has ever faced the problem. I have also tried different setting but couldn't manage to solve the problem.

    Your help is always appreciated.

    Many thanks in advance.

    Regards

  • #2
    can you try the newest Pindel version at
    github.com/genome/pindel

    Comment


    • #3
      Hi Kai,

      I will try to run that and let you know what's going on. In past I had difficulties installing Pindel in my local machine. However, my admin installed it for me. I will give another try by myself and if not will request the admin. I will keep you posted.

      Regards

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