• https://mixcr.readthedocs.org/en/latest/

• Module Name: mixcr (see the modules page for more information)
• Multithreaded

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

[user@biowulf]$ sinteractive --cpus-per-task=4 --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 ~]$ module load mixcr

[user@cn3144 ~]$ mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK \
		/data/$USER/S1.fastq.gz \
		/data/$USER/S2.fastq.gz \
		aln.vdjca 

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load mixcr
mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK \
		/data/$USER/S1.fastq.gz \
		/data/$USER/S2.fastq.gz \
		aln.vdjca

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g mixcr.sh

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

cd /data/$USER/dir1; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK S1.fastq.gz S2.fastq.gz aln.vdjca
cd /data/$USER/dir2; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK S1.fastq.gz S2.fastq.gz aln.vdjca
cd /data/$USER/dir3; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK S1.fastq.gz S2.fastq.gz aln.vdjca
cd /data/$USER/dir4; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK S1.fastq.gz S2.fastq.gz aln.vdjca

Submit this job using the swarm command.

swarm -f mixcr.swarm -g 10 -t 4 --module mixcr