Biowulf High Performance Computing at the NIH
MutSig2CV on Biowulf

mutsig2cv analyzes somatic point mutations discovered in DNA sequencing, identifying genes mutated more often than expected by chance.

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 --mem=10g
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 ~]$
[user@cn3144 ~]$ ml MutSig
[user@cn3144 ~]$ MutSigCV \
$MUTSIG_EX/LUSC.mutations.maf \
$MUTSIG_REF/exome_full192.coverage.txt \
$MUTSIG_REF/gene.covariates.txt \
output \
$MUTSIG_REF/mutation_type_dictionary_file.txt \
$MUTSIG_REF/chr_files_hg19
[user@cn3144 ~]$ ls -l
-rw-r--r-- 1 user user      510 Aug 29 12:47 output.categs.txt
-rw-r--r-- 1 user user  8989673 Aug 29 12:47 output.coverage.txt
-rw-r--r-- 1 user user 38760466 Aug 29 12:47 output.mutations.txt
-rw-r--r-- 1 user user      750 Aug 29 12:43 output.mutcateg_discovery.txt
-rw-r--r-- 1 user user  1397350 Aug 29 13:09 output.sig_genes.txt
[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. MutSig.sh). For example:

#!/bin/bash
module load MutSig
MutSigCV \
  $MUTSIG_EX/LUSC.mutations.maf \
  $MUTSIG_REF/exome_full192.coverage.txt \
  $MUTSIG_REF/gene.covariates.txt \
  output \
  $MUTSIG_REF/mutation_type_dictionary_file.txt \
  $MUTSIG_REF/chr_files_hg19

Submit this job using the Slurm sbatch command.

sbatch --mem=10g MutSig.sh
10 GB memory is sufficient for this example job. You may need to increase the memory allocation for your own MutSig jobs.