Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Error when running Dindel realignment stage

    Hi all,

    I'm running Dindel for calling small indels from whole-exome sequencing data.
    I have finished pervious samples successfully. However, when I try to run another 13 samples, I got an error message at the stage 3:

    matepos inconsistency!
    14647035 14646905

    So, there is nothing in the .glf.txt file and .vcf file.
    This error happens on all the BAM files at the first realignment window.
    I have got the .variants.txt file and .library file successfully.

    Here is the command I used in stage 3:
    ./dindel-1.01-linux-64bit --analysis indels --doDiploid --bamFile chr22_17737.fa_sort.bam --ref ~/hg18/chr22.fa --varFile chr22_17737.fa.1.txt --libFile chr22_17737.fa.libraries.txt --outputFile chr22_17737.fa > chr22_17737.fa.out 2> chr22_17737.fa.err

    In the screen output for stage 3, it stopped at:
    ****
    tid: chr22 pos: 14646919 leftPos: 14646860 rightPos: 14646979
    Fetching reads....

    Maybe there is a problem when fetching reads from the BAM files caused by "matepos inconsistency"?

    Is there anyone can help me?
    Many thanks!

  • #2
    Problem have been solved.
    This error is caused by pair1 and pair2 fastq files are not in the same order.

    Comment


    • #3
      How did you solve the problem??

      Dear ywy25,
      con you explain exactly how you solved the problem you mentioned in the previous post?
      I have the same problem, but I'm not understanding.
      I am perfectly aware of the fact that the discussion goes back more than two years ago...anyway I hope in you have a great memory...
      Many thanks

      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
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X