Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bfast alignment error

    The command I am using is :
    "./bfast-0.7.0/bin/bfast match -f human_g1k_v37.fa -r part2.fa > test.bmf"

    The human_g1k_v37.fa has been indexed.

    Error Message:
    “In function "RGIndexReadHeader": Fatal Error[ReadFileError]. Message: Could not read header.”

    Dose somebody have encountered this error? Or can you give some ideas on what may be the reason for this error?

    The input is indexed fasta and fastq. I don't think there is read header in these inputs. Read header, as I know, appears in SAM or BAM format files, which are output of alignment. But now I am working on alignment, how can the inputs have read header. It's strange.

  • #2
    It means "read" as in trying to "read" the header, not the noun read

    There is not enough information to diagnose the problem.

    Comment


    • #3
      Thanks for your pointing out "read" is a verb . I have to admit my poor English reading.

      "There is not enough information to diagnose the problem." Actually, all information I know related to this problem was listed. I have emailed to authors of this software, but haven't received any answer.

      So except hacking the source code, I don't have other approaches yet.

      Comment


      • #4
        I am the author of the software. Unfortunately, I maintain this software on my free time and my free time has asymptotically approached zero lately so I have been unable to debug the software. Also, I don't have a machine that can index a human genome at home, so perhaps I should start a donation drive to get one and better support BFAST users?

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Genetic Variation in Immunogenetics and Antibody Diversity
          by seqadmin



          The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
          11-06-2024, 07:24 PM
        • seqadmin
          Choosing Between NGS and qPCR
          by seqadmin



          Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
          10-18-2024, 07:11 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 11:09 AM
        0 responses
        22 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Today, 06:13 AM
        0 responses
        20 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-01-2024, 06:09 AM
        0 responses
        30 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-30-2024, 05:31 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Working...
        X