Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • MIRA question

    Hi all,

    I'm trying to make contigs out of Illumina transcriptome data using MIRA but I keep getting an error.

    Command used:
    Code:
    mira -fastq=SRR016565_1.fastq -project=Project --job=denovo,est,normal,solid -lowqualitydata -LR:external_quality=none -LR:load_sequence_data=yes
    Error:
    Code:
    Internal logic/programming/debugging error (*sigh* this should not have happened).
    Please contact the author: [email protected]
    "No input to load or no sequences in input files? Did you provide data to load?"
    ->Thrown: void Assembly::loadSequenceData()
    ->Caught: main
    Program aborted.
    CWD: /home/labgroup/Desktop/Project_Illumina_transcriptome_data
    Aborted
    Can anyone tell me what I'm doing wrong? My intput files are fastq formatted like this:
    Code:
    @SRR016565.84 BI:081230_SL-XAQ_0001_FC30M3RAAXX:2:1:1:1475 length=76
    NTAANGCTTAGGGCGTGGCNNTTGNTTTTTTGTAGTTAATGTGAACAGTTTTAACTCATTGANNACTCANNTNCCG
    +SRR016565.84 BI:081230_SL-XAQ_0001_FC30M3RAAXX:2:1:1:1475 length=76
    !)99!//3//;3+#3%I6)!!8.A!0&9(0)(0.5%,&041+/0)+*-'&1,-1*2'*+%*.!!+*,+%!!&!'(%
    Thanks!
    Kevin

  • #2
    I'd have asked on the MIRA mailing list - the author seems very responsive:


    You should also give the precise version of MIRA you are using, and other details like the OS could be important.

    Comment


    • #3
      Thanks,

      I'll try the mailing list. I was hoping it was something really silly I was forgetting.

      FWIW, I'm using Ubuntu 9.10 and I have the most recent version of MIRA as of yesterday.

      Thanks,
      Kevin

      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
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 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
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X