Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • dinesh21.ksd
    Junior Member
    • Dec 2014
    • 4

    #1

    Trinity denovo assemply error

    hai, i am a newbie in linux. but i need denova assembly form trinity for my research work.

    first i am install Trinity in my system. after the complete installation i try this command

    ./Trinity --seqType fq --max_memory 8G --single ~/Desktop/worm\ transcript/R133-L7-P07-AGTCAA-Sequences.fq --CPU 8

    but after 3-5 sec whole assembly was stopped and show this following error

    Trinity version: v2.0.6
    sh: 1: curl: not found
    sh: 1: curl: not found
    -ERROR: couldn't run the network check to confirm latest Trinity software version.

    Thursday, July 16, 2015: 11:06:57 CMD: java -Xmx64m -jar /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
    Thursday, July 16, 2015: 11:06:57 CMD: java -Xmx64m -jar /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1


    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
    ----------------------------------------------------------------------------------

    Use of uninitialized value in array dereference at ./Trinity line 1251.
    ----------------------------------------------
    --------------- Inchworm ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------

    Thursday, July 16, 2015: 11:06:57 CMD: /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 6 --PARALLEL_IWORM > /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp 2>/dev/null
    Thursday, July 16, 2015: 11:06:57 CMD: touch /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.finished
    ERROR, no butterfly assemblies reported. at ./Trinity line 1149.


    i think there is no installation problem in Trinity software. i am not familiar in linux. so someone pls help me to solve this problem.

    and i know my English is very poor. so pls understand my problem and help me

Latest Articles

Collapse

  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2




    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
    Yesterday, 06:46 AM
  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
29 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-28-2026, 09:51 AM
0 responses
20 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
71 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
48 views
0 reactions
Last Post SEQadmin2  
Working...