Biowulf High Performance Computing at the NIH
OPERA-LG on Biowulf

OPERA (Optimal Paired-End Read Assembler) is a sequence assembly program. It uses information from paired-end/mate-pair/long reads to order and orient the intermediate contigs/scaffolds assembled in a genome assembly project, in a process known as Scaffolding. OPERA is based on an exact algorithm that is guaranteed to minimize the discordance of scaffolds with the information provided by the paired-end/mate-pair/long reads.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load opera-lg
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 ~]$ tar xzf $OPERA_EXAMPLES/test_dataset.tar.gz
[user@cn3144 ~]$ OPERA-LG test_dataset/multiLib.config

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. opera-lg.sh). For example:

#!/bin/bash
module load opera-lg
tar xzf $OPERA_EXAMPLES/test_dataset_long_reads.tar.gz
OPERA-long-read.pl \
  --contig-file test_dataset_long_reads/contigs.fa \
  --illumina-read1 test_dataset_long_reads/illumina_1.fastq.gz \
  --illumina-read2 test_dataset_long_reads/illumina_2.fastq.gz \
  --long-read-file test_dataset_long_reads/nanopore.fa \
  --output-prefix opera-lr --output-directory RESULTS

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] opera-lg.sh