Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bad hash size error in Jellyfish

    Hi all,

    I'm using Trinity for the first time on some data we've been sent by a colleague. I'm getting this error during the Jellyfish stage - I wondered if any of you have any insights?

    Here's the error:

    perl Trinity.pl --seqType fq --JM 30G --single ../../../../data/Easp_VT.fastq --CPU 4
    Current settings:
    time(seconds) unlimited
    file(blocks) unlimited
    data(kbytes) unlimited
    stack(kbytes) 8192
    coredump(blocks) 0
    memory(kbytes) unlimited
    locked memory(kbytes) 64
    process unlimited
    nofiles 1024
    vmemory(kbytes) unlimited
    locks unlimited


    -since butterfly will eventually be run, lets test for proper execution of java
    #######################################
    Running Java Tests
    Thursday, January 23, 2014: 10:05:30 CMD: java -Xmx64m -jar /Trinity/util/ExitTester.jar 0
    CMD finished (0 seconds)
    Thursday, January 23, 2014: 10:05:30 CMD: java -Xmx64m -jar /Trinity/util/ExitTester.jar 1
    -we properly captured the java failure status, as needed. Looking good.
    Java tests succeeded.
    ###################################

    -------------------------------------------
    ----------- Jellyfish --------------------
    -- (building a k-mer catalog from reads) --
    -------------------------------------------

    Thursday, January 23, 2014: 10:05:55 CMD: /Trinity/trinity-plugins/jellyfish/bin/jellyfish count -t 4 -m 25 -s 409974768 single.fa
    CMD finished (2344 seconds)
    Thursday, January 23, 2014: 10:44:59 CMD: /Trinity/trinity-plugins/jellyfish/bin/jellyfish merge -o jellyfish.kmer.db mer_counts_0 mer_counts_1 mer_counts_2 mer_counts_3 mer_counts_4 mer_counts_5 mer_counts_6 mer_counts_7 mer_counts_8 mer_counts_9
    terminate called after throwing an instance of 'jellyfish::compacted_hash::ErrorReading'
    what(): 'mer_counts_0': Bad hash size '4467145872', expected '4494027120' bytes
    Error, cmd: /Trinity/trinity-plugins/jellyfish/bin/jellyfish merge -o jellyfish.kmer.db mer_counts_0 mer_counts_1 mer_counts_2 mer_counts_3 mer_counts_4 mer_counts_5 mer_counts_6 mer_counts_7 mer_counts_8 mer_counts_9 died with ret 6 at Trinity.pl line 1793.

  • #2
    You *may* be running out of memory. What is the memory size in your system? Using a small '-JM' size could be useful. It should only increase the time to run Jellyfish by a small amount.

    Comment


    • #3
      I'd also check the version of perl, some older versions have a memory cap.

      Comment


      • #4
        Thanks, it does appear to have been a memory problem and reducing the -Jm seems to have solved it.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Recent Advances in Sequencing Technologies
          by seqadmin







          Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

          Long-Read Sequencing
          Long-read sequencing has...
          12-02-2024, 01:49 PM
        • seqadmin
          Genetic Variation in Immunogenetics and Antibody Diversity
          by seqadmin



          The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
          11-06-2024, 07:24 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 12-02-2024, 09:29 AM
        0 responses
        145 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 12-02-2024, 09:06 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 12-02-2024, 08:03 AM
        0 responses
        42 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-22-2024, 07:36 AM
        0 responses
        72 views
        0 likes
        Last Post seqadmin  
        Working...
        X