Biowulf High Performance Computing at the NIH
Slamdunk on Biowulf

Streamlining SLAMseq analysis with ultra-high sensitivity: SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.


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 --cpus-per-task=8 --mem=20g --gres=lscratch:20
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 slamdunk

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ cp /fdb/genome/hg19/chr_all.fa .

[user@cn3144 ~]$ slamdunk all -r chr_all.fa -b ./exampleBAM.bed \
      -o out -t $SLURM_CPUS_PER_TASK ./exampleBAM.bam
slamdunk all
Running slamDunk map for 1 files (8 threads)
Running slamDunk sam2bam for 1 files (8 threads)
Creating output directory: out/filter
Running slamDunk filter for 1 files (8 threads)

[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. For example:

set -e
module load slamdunk
cd /lscratch/$SLURM_JOB_ID
cp /fdb/genome/hg19/chr_all.fa .
slamdunk all -r chr_all.fa -b ./exampleBAM.bed \
             -o out -t $SLURM_CPUS_PER_TASK ./exampleBAM.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] [--gres=lscratch:#]