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  • JManuelMonroyKuhn
    Member
    • Oct 2014
    • 25

    #1

    Oases error

    Hello!!
    I'm trying to run Oases to see if I properly installed it on a cluster.
    I ran it using the python script

    python /home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py -m 21 -M 25 -s 2 -o PE_assembly -d '-fastq -shortPaired -separate /home/hpc/uj502/di29kiz/reads.right.fq /home/hpc/uj502/di29kiz/reads.left.fq' -p '-ins_length 259 -min_trans_lgth_100'

    I got this error

    Traceback (most recent call last):
    File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 121, in <module>
    main()
    File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 115, in main
    singleKAssemblies(options)
    File "/home/hpc/uj502/di29kiz/oases_0.2.8/scripts/oases_pipeline.py", line 46, in singleKAssemblies
    assert p.returncode == 0, "Oases failed at k = %i\n%s" % (k, output[0])
    AssertionError: Oases failed at k = 21
    Unusual number of arguments!

    What can be the problem?
    Thanks
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Remind us if you are using a job scheduler to run this job and if so which scheduler are you using?

    Comment

    • JManuelMonroyKuhn
      Member
      • Oct 2014
      • 25

      #3
      Job scheduler? I do not know that. These are the previous commands for the submission on the cluster

      #!/bin/bash
      #SBATCH -o /home/hpc/uj502/di29kiz/OASEStry.%j.%N.out
      #SBATCH -D /home/hpc/uj502/di29kiz/oases_0.2.8
      #SBATCH -J OASEStry
      #SBATCH --get-user-env
      #SBATCH --clusters=uv3
      #SBATCH --cpus-per-task=4
      #SBATCH --mail-type=all
      #SBATCH --export=PATH
      #SBATCH --time=12:00:00
      source /etc/profile.d/modules.sh

      Comment

      • JManuelMonroyKuhn
        Member
        • Oct 2014
        • 25

        #4
        I tried again and now it worked :/
        I don't know what was wrong, thanks anyway

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142

          #5
          You are using a job scheduler/resource manager. Likely SLURM.

          Comment

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