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  • Trinity - Jellyfish apparently blocking

    Hi everybody,
    I am running trinity v2.0.6 with miseq illumina PE reads (1.4-4M reads) on a 12CPU-24Gb RAM workstation.
    Sometimes I get trinity working fine in an home-made pipeline, but often it idles at the first phase, as follows:

    Code:
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer catalog from reads) --
    -------------------------------------------
    
    Tuesday, December 22, 2015: 12:40:46	CMD: /home/gimto/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish count -t 6 -m 25 -s 2968824912  --canonical  both.fa
    I let it run for also a day without any change. When i kill the process, I still see jellyfish run as zombie process.
    It is not strictly correlated to the input files, since after reboot, I rerun trinity on the same files and I got it work.
    The trinity command is this:
    Code:
    Trinity --seqType fq --max_memory 20G --left F1.trimmed.fastq --right R1.trimmed.fastq --CPU 6 --min_contig_length 300 --bypass_java_version_check --verbose --output ./trinity_out_dir
    Any suggestion? May it be due to memory? Should I wait more? On trinity manual, jellyfish should take about one hour (on the samples that I got running, it takes a few minutes, but when it doesn't work, it takes also more than 24h).
    Thank you in advance!

  • #2
    I have same problem on 32CPU - 256GB RAM workstation.(not my server)(pedora)

    when I runned Trinity on 8CPU - 256GB RAM workstation (my server)(ubuntu), its jellyfish ended just 15~20min and running inchworm normally.

    what is problem?

    Comment

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