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

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=8g
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 /data/${USER}
[user@cn3144 ~]$ 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 ~]$ rm MutSigCV_example_data.1.0.1.zip
[user@cn3144 ~]$ cp /usr/local/apps/mutsig2cv/DOWNLOADS/reference.tar.gz .
[user@cn3144 ~]$ tar -xzf reference.tar.gz
[user@cn3144 ~]$ rm reference.tar.gz
[user@cn3144 ~]$ run_MutSig2CV.sh /usr/local/matlab-compiler/v81 MutSigCV_example_data.1.0.1.zip/LUSC.mutations.maf 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 ~]$

Create a batch input file (e.g. mutsig2cv.sh). For example:

#!/bin/bash

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
cp /usr/local/matlab-compiler/v81.tar.gz .
tar -xzf v81.tar.gz
cp /usr/local/apps/mutsig2cv/DOWNLOADS/reference.tar.gz .
tar -xzf reference.tar.gz
run_MutSig2CV.sh v81 MutSigCV_example_data.1.0.1/LUSC.mutations.maf OUTPUT

Submit this job using the Slurm sbatch command.

sbatch --mem=10g --gres=lscratch:100 mutsig2cv.sh