Biowulf High Performance Computing at the NIH
cgpBattenberg on Biowulf

An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data.

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. Note that the cgpBattenberg.pl is part of the cancerit-wgs tools.

[user@biowulf]$ sinteractive --cpus-per-task=4
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 cgpBattenberg
Usage:
    battenberg.pl [options]

      Required parameters:
        -outdir                -o   Folder to output result to.
        -reference             -r   Path to reference genome index file *.fai
        -tumbam                -tb  Path to tumour bam file
                                     - when '-a' defined sample name
        -normbam               -nb  Path to normal bam file
                                     - when '-a' defined sample name
        -gender                -ge  Gender, XX, XY or L (see -gl)
        -impute-info           -e   Location of the impute info file
        -thousand-genomes-loc  -u   Location of the directory containing 1k genomes data
        -ignore-contigs-file   -ig  File containing contigs to ignore
                                    - specifically male sex chromosome, mitochondria and non primary contigs
        -gc-correction-loc     -gc  Path to gc correction files

      Optional parameters:
[...snip...]

[user@cn3144]$ battenberg.pl -p output \
    -r /fdb/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa \
    -tb tumor.bam \
    -nb normal.bam \
    -ge XX \
    -impute-info /fdb/cancerit-wgs/cgpBattenberg/impute/impute_info.txt \
    -thousand-genomes-loc /fdb/cancerit-wgs/cgpBattenberg/1000genomesloci \
    -ignore-contigs-file ignore_contigs \
    -gc-correction-loc /fdb/cancerit-wgs/cgpBattenberg/battenberg_wgs_gc_correction_1000g_v3 \
    -species Human -assembly 37 \
    -t $SLURM_CPUS_PER_TASK


[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. cgpBattenberg.sh), which uses the input file 'cgpBattenberg.in'. For example:

#!/bin/bash
module load cgpBattenberg
battenberg.pl -p output \
    -r /fdb/igenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa \
    -tb tumor.bam \
    -nb normal.bam \
    -ge XX \
    -impute-info /fdb/cancerit-wgs/cgpBattenberg/impute/impute_info.txt \
    -thousand-genomes-loc /fdb/cancerit-wgs/cgpBattenberg/1000genomesloci \
    -ignore-contigs-file ignore_contigs \
    -gc-correction-loc /fdb/cancerit-wgs/cgpBattenberg/battenberg_wgs_gc_correction_1000g_v3 \
    -species Human -assembly 37 \
    -t $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=30g cgpBattenberg.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. cgpBattenberg.swarm). For example:

battenberg.pl -p output -tb tumor1.bam -nb normal1.bam ... -t $SLURM_CPUS_PER_TASK 
battenberg.pl -p output -tb tumor2.bam -nb normal2.bam ... -t $SLURM_CPUS_PER_TASK 
battenberg.pl -p output -tb tumor3.bam -nb normal3.bam ... -t $SLURM_CPUS_PER_TASK 

Submit this job using the swarm command.

swarm -f cgpBattenberg.swarm -g 30 -t 16 --module cgpBattenberg
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module cgpBattenberg Loads the cgpBattenberg module for each subjob in the swarm