Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Trinity error

    Hello,

    I am trying to do assembly through Trinity but i am getting this error during Chrysalis running. PLease help me out to rectify this error.

    Thank You


    -----------------------------------------
    --- Chrysalis: GraphFromFasta -----------
    -- (cluster related inchworm contigs) ---
    -----------------------------------------

    -setting num threads to: 2
    -running on 2 threads
    GraphFromFasta: Reading file: /ddnB/work/mverma/New_Data/Tuu_Gia_M_fijiensis_24_hpi_trinity_output/inchworm.K25.L25.DS.fa
    done!
    Counting k-mers...
    KmerAlignCore- Contigs: 1038967
    done, assigning k-mers...
    KmerAlignCore- Contigs: 1038967
    done!
    -setting omp for schedule chunksize to 5194 for 1038968 iworm contigs
    Phase 1: Collecting candidate weldmers between iworm contig pairs sharing k-1mers
    Processed: 99.9999 % of iworm contigs.

    ...done Phase 1. (447.19 seconds)
    Captured: 1341537 weldmer candidates.
    Setting up reads for streaming...
    Identifying reads that support welding of iworm contigs...
    Reads: (unknown count: streaming-mode)

    Message from root@mike1 on <no tty> at 15:15 ...
    User mverma process GraphFromFasta killed >30 min, using 3% of memory
    EOF
    sh: line 1: 36680 Killed /home/packages/bioinformatics/trinityrnaseq/2.0.6/Intel-13.0.0/Chrysalis/GraphFromFasta -i /ddnB/work/mverma/New_Data/Tuu_Gia_M_fijiensis_24_hpi_trinity_output/inchworm.K25.L25.DS.fa -r single.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 2 -k 24 -kk 48 > /ddnB/work/mverma/New_Data/trinity_output/chrysalis/GraphFromIwormFasta.out
    Trinity run failed. Must investigate error above.

  • #2
    It sounds like your job was purposely cancelled after 30 minutes. This is probably because the server you are using has a job scheduling system, e.g., SLURM. With these systems, you need to write a shell script requesting a certain amount of memory and time, then your job will run when it gets to the top of the "queue".

    Maybe you could email the administrator (Mike?) and ask how it works.

    Good luck!

    Matt.

    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
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    57 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    70 views
    0 likes
    Last Post seqadmin  
    Working...
    X