DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.
Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.
biowulf $ qsub -I -l nodes=1:g24:c24 qsub: waiting for job 2236960.biobos to start qsub: job 2236960.biobos ready [user@pXXX]$ module load delly [user@pXXX]$ cd /data/$USER/XXXX [user@pXXX]$ delly lib1.bam lib2.bam libN.bam [user@pXXX]$ exit qsub: job 2236960.biobos completed user@biowulf]$
1. Create a script file along with the lines below. Modify the path of location before running.
#!/bin/bash # This file is runDelly # #PBS -N delly #PBS -m be #PBS -k oe module load delly cd /data/$USER//run1 delly lib1.bam lib2.bam libN.bam
3. Submit the script using the 'qsub' command on Biowulf
$ qsub -l nodes=1:g8 /data/$USER/runDelly
Submitting a swarm of delly jobs
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:
cd /data/$USER/run1; delly lib1.bam lib2.bam libN.bam
cd /data/$USER/run2; delly lib1.bam lib2.bam libN.bam
........ ........ cd /data/$USER/run20; delly lib1.bam lib2.bam libN.bam
The '-f' and '--module' options for swarm are required
- -f: the swarm command file name above (required)
- --module: load the preserves the environment variables for the swarm jobs
- -g: gb of memory needed for each line of the commands in the swarm file above.(optional)
By default, each line of the command file above will be executed on 1 processor core of a node and use 1gb of memory. If this is not what you want, you will need to specify '-t' and '-g' flags when you submit the job on biowulf.
Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:
biowulf> $ swarm -g 10 -f cmdfile --module delly
For more information regarding running swarm, see swarm.html