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  • Oases/Velvet

    Hello!
    I am running Oases/Velvet for a de novo transcriptome assembly. My data is large, around 350 million paired reads.

    This is how I ran it on the cluster I am using. (SLURM)

    #!/bin/bash
    #SBATCH -o /home/hpc/uj502/di29kiz/OASESLA2750.%j.%N.out
    #SBATCH -D /home/hpc/uj502/di29kiz/oases_0.2.8
    #SBATCH -J OASESLA2750
    #SBATCH --get-user-env
    #SBATCH --clusters=uv3
    #SBATCH --cpus-per-task=300
    #SBATCH --mail-type=all
    #SBATCH --export=PATH
    #SBATCH --time=48:00:00
    source /etc/profile.d/modules.sh


    python /home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py -m 25 -M 45 -s 2 -o '/naslx/projects/uj502/di29kiz/oases/LA2750' -d '-fastq -shortPaired -separate /naslx/projects/uj502/di29kiz/libraries/NG-7404_LA2750tpool1p.fastq /naslx/projects/uj502/di29kiz/libraries/NG-7404_LA2750tpool2p.fastq' -p '-ins_length 229'

    My problem is regarding time, I only have 48 hours of running time on the cluster per submitted job. It does not make it on time. Any suggestions?
    I am also not sure if it is running properly, how can I see what OASES/Velvet is doing? I only can see on the output folder three files

    Log Roadmaps Sequences


    Cheers

  • #2
    I have not used Oases,

    but when you run velvet, first you run velveth, which produces 3 files - Log, Roadmaps, and Sequences - and then velvetg which produces several other files.

    this suggests that your program has made it through the velveth stage.

    Comment


    • #3
      Is 48h the max you can get on this cluster?

      You may want to try a sub-sampled dataset (100 million reads or less) to see if it makes it through to the end.

      Comment

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