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 --gres=lscratch:100
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 ~]$ cd /lscratch/${SLURM_JOB_ID}
[user@cn3144 ~]$ module load mutsig2cv
[user@cn3144 ~]$ cp /usr/local/apps/mutsig2cv/TEST_DATA/MutSigCV_example_data.1.0.1.zip .
[user@cn3144 ~]$ unzip MutSigCV_example_data.1.0.1.zip
[user@cn3144 ~]$ cd MutSigCV_example_data.1.0.1
[user@cn3144 ~]$ cp /usr/local/matlab-compiler/v81.tar.gz .
[user@cn3144 ~]$ tar -xzf v81.tar.gz
[user@cn3144 ~]$ cp /usr/local/apps/mutsig2cv/3.11/reference.tar.gz .
[user@cn3144 ~]$ tar -xzf reference.tar.gz
[user@cn3144 ~]$ run_MutSig2CV.sh v81 LUSC.mutations.maf TEST_OUTPUT
[...]
16:16:47  16:41:52  8187/18862 ITGA9       3       1000  CV 0.617212 CL 1.000000 FN 0.326000  [625  81   10   1    0    1]
16:16:47  16:41:53  8188/18862 ITGAD       9       1000  CV 0.470805 CL 1.000000 FN 0.349000  [625  81   10   1    0    1]
16:16:48  16:41:53  8189/18862 ITGAE       4       1000  CV 0.918407 CL 1.000000 FN 0.731000  [625  81   10   1    0    1]
16:16:48  16:41:53  8190/18862 ITGAL       1          0  CV 0.998619 CL 1.000000 FN 1.000000  [625  81   10   1    0    1]
16:16:48  16:41:53  8191/18862 ITGAM       7       1000  CV 0.653397 CL 1.000000 FN 0.068000  [625  81   10   1    0    1]
16:16:48  16:41:54  8192/18862 ITGAV       4       1000  CV 0.849691 CL 1.000000 FN 0.100000  [626  81   10   1    0    1]
16:16:48  16:41:54  8193/18862 ITGAX       8       1000  CV 0.410713 CL 1.000000 FN 0.885000  [627  81   10   1    0    1]
16:16:52  16:41:56  8210/18862 ITIH4       2       1000  CV 0.872721 CL 1.000000 FN 0.698000  [629  82   10   1    0    1]
16:16:52  16:41:56  8211/18862 ITIH5       5       1000  CV 0.717304 CL 1.000000 FN 0.729000  [629  82   10   1    0    1]
[...]
16:44:08  16:44:08 18860/18862 ZYX         1          0  CV 0.817634 CL 1.000000 FN 1.000000  [1591 184  19   4    1    7]
16:44:08  16:44:08 18861/18862 ZZEF1       2       1000  CV 0.980706 CL 1.000000 FN 0.500000  [1591 184  19   4    1    7]
16:44:08  16:44:08 18862/18862 ZZZ3        6       1000  CV 0.302995 CL 0.055000 FN 0.507000  [1591 184  19   4    1    7]

9 genes with q<=0.1
Saving results...   [save_struct] 38/70 39/70 40/70 41/70 42/70 43/70 44/70 45/70 46/70 47/70 48/70 49/70 50/70 51/70 52/70 
53/70 54/70 55/70 56/70 57/70 58/70 59/70 60/70 61/70 62/70 63/70 64/70 65/70 66/70 67/70 68/70 69/70 70/70  [collapse] [write]
Done.

[user@cn3144 ~]$ 
[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. mutsig2cv.sh). For example:

#!/bin/bash
set -e
module load mutsig2cv
cd /lscratch/${SLURM_JOB_ID}
cp /usr/local/apps/mutsig2cv/TEST_DATA/MutSigCV_example_data.1.0.1.zip .
unzip MutSigCV_example_data.1.0.1.zip
cd MutSigCV_example_data.1.0.1
cp /usr/local/matlab-compiler/v81.tar.gz .
tar -xzf v81.tar.gz
cp /usr/local/apps/mutsig2cv/3.11/reference.tar.gz .
tar -xzf reference.tar.gz
run_MutSig2CV.sh v81 LUSC.mutations.maf TEST_OUTPUT

Submit this job using the Slurm sbatch command.

sbatch --mem=10g --gres=lscratch:100 mutsig2cv.sh
10 GB memory is sufficient for this example job. You may need to increase the memory allocation for your own jobs.