Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie2 input read error

    Hi All

    Bowtie2 is not able to recognize my paired end data input. Seems to be a command line related error but I checked the fastqs anyway and both appear to be fine and properly paired. Note the rendering of the command line in the error. Any idea whats wrong?

    Thanks

    Mark

    Code:
    $  /usr/local/thirdparty/bowtie2/bowtie2-2.1.0/bowtie2 --no-mixed --no-discordant --no-dovetail --no-contain --sensitive-local -I 151 -X 700 -x dataset_18153.dat  -1 A9_S1_L001_R1_001_val_1.10000.10000.fq -2 A9_S1_L001_R2_001_val_2.10000.10000.fq -S -1509026240-bowtie2.sam
    
    Error: 0 mate files/sequences were specified with -1, but 1
    mate files/sequences were specified with -2.  The same number of mate files/
    sequences must be specified with -1 and -2.
    Error: Encountered internal Bowtie 2 exception (#1)
    Command: /usr/local/thirdparty/bowtie2/bowtie2-2.1.0/bowtie2-align --wrapper basic-0 --no-mixed --no-discordant --no-dovetail --no-contain --sensitive-local -I 151 -X 700 -x dataset_18153.dat -S -1 -2 A9_S1_L001_R2_001_val_2.10000.10000.fq A9_S1_L001_R1_001_val_1.10000.10000.fq,509026240-bowtie2.sam
    bowtie2-align exited with value 1

  • #2
    Nevermind, I spotted it. This command-line, which was generated programmatically, contains the following erroneous argument.

    -S -1509026240-bowtie2.sam

    The hypen in "-1509026240-bowtie2.sam" is the culprit.

    Thanks anyway

    Mark

    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, 03-27-2024, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X