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Old 11-11-2014, 03:56 AM   #1
JManuelMonroyKuhn
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Location: Munich

Join Date: Oct 2014
Posts: 25
Question 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
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Old 11-11-2014, 04:02 AM   #2
GenoMax
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Remind us if you are using a job scheduler to run this job and if so which scheduler are you using?
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Old 11-11-2014, 04:10 AM   #3
JManuelMonroyKuhn
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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
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Old 11-11-2014, 04:16 AM   #4
JManuelMonroyKuhn
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I tried again and now it worked :/
I don't know what was wrong, thanks anyway
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Old 11-11-2014, 04:41 AM   #5
GenoMax
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You are using a job scheduler/resource manager. Likely SLURM.
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