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.
References:
- Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets, Neumann, T., Herzog, V. A. et al. BMC Bioinformatics, 20(1), 258, 2019.
Documentation
Important Notes
- Module Name: slamdunk (see the modules page for more information)
- Multithreaded
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. slamdunk.sh). For example:
#!/bin/bash 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:#] slamdunk.sh