Oases/Velvet

[JManuelMonroyKuhn]

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

[mastal]

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.

[GenoMax]

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.