Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Mark
    replied
    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

    Leave a comment:


  • Mark
    started a topic Bowtie2 input read error

    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

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-23-2024, 04:11 PM
1 response
22 views
0 likes
Last Post kim897
by kim897
 
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
26 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
58 views
0 likes
Last Post seqadmin  
Working...
X