Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • trinity runing error

    Hi everyone,

    The RAM of my computer is 32GB and the size of my data is about 66GB. I set --JM 20G, --CPU. the Chrysalis process failed:

    -------------------
    ---- Chrysalis ----
    -------------------

    mkdir: cannot create directory `/home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/chrysalis': File exists
    ###########################################################
    ## Running Bowtie to map fragment ends to Inchworm Contigs
    ## to use pairing info for Chrysalis' clustering
    ###############################################################

    CMD: ln -sf /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/inchworm.K25.L25.DS.fa target.fa
    CMD: bowtie-build -q target.fa target
    CMD: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead -f target both.fa > bowtie.out
    Reads file contained a pattern with more than 1024 sequence characters.
    Please truncate reads and quality values and and re-run Bowtie.
    Offending read: FCC327Identical(self):
    terminate called after throwing an instance of 'int'
    Aborted (core dumped)
    COMMAND: bowtie -a -m 20 --best --strata --threads 6 --quiet --chunkmbs 512 -q -S --sam-nohead -f target both.fa > bowtie.out
    Died with exit code 34304
    Exiting.
    time(seconds) unlimited
    file(blocks) unlimited
    data(kbytes) unlimited
    stack(kbytes) 8192
    coredump(blocks) 0
    memory(kbytes) unlimited
    locked memory(kbytes) 64
    process 256334
    nofiles 1024
    vmemory(kbytes) unlimited
    locks unlimited

    Error, the Chrysalis process failed:
    Error, cmd: /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/Chrysalis/Chrysalis -i both.fa -iworm /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/inchworm.K25.L25.DS.fa -o /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/AS/chrysalis -cpu 6 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 200000 -sort_buffer_size 20G -max_mem_reads 10000000 -paired -reads_for_pairs both.fa -butterfly /home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/Butterfly/Butterfly.jar 2>&1 died with ret 65280 at Trinity.pl line 1793.

    at Trinity.pl line 1322
    main::run_chrysalis('/home/chaganti/Desktop/Rao/Software/trinityrnaseq_r20131110/A...', 'both.fa', 200, 500, undef, 'both.fa') called at Trinity.pl line 1136

    Does anybody know how to solve the problem?

    Thank you very much!

    Tom

  • #2
    Before I run all the sequences, I run only 1 sample (1 left file, 1 right file, 6.6GB in total) and it worked.

    Comment


    • #3
      I have not much experience in running Trinity, but from your logfile it seems that Bowtie existed abnormally and this also caused the Perl wrapper of Trinity to exit. Maybe you should have a closer look at the bowtie.out file, what caused the error.

      Comment


      • #4
        Does anybody have experience in running 70GB data in a computer with 32GB ram?

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM
        • 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

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        28 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        24 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        52 views
        0 likes
        Last Post seqadmin  
        Working...
        X