Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BFAST match abort trap

    Hello,

    I am trying to analyze SOLiD data using BFAST, and am a little new to the system. I have successfully created and indexed the reference genome, but I am running into problems with BFAST match. I get an error message saying:

    Reading /ResearchFiles/JEC21_genome/CNA_assembly/BFAST/NIH433_fastq_reads.1.fastq into a temp file.
    Assertion failed: (m->readLength > 0), function RGMatchPrint, file ../bfast/RGMatch.c, line 155.
    Abort trap

    My command line is bfast match -f JEC21_all.fasta -r NIH433_fastq_reads.1.fastq > NIH433_JEC21_matched

    I also created the input fastq file using the solid2fastq program that came with the BFAST package.

    Any idea what is causing this?

    Thanks,

    BB

  • #2
    Most likely the input fastq is corrupted. You can either try to re-run solid2fastq, or remove reads from the input fastq until you find the offending read.

    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
    9 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