Mixcr on Biowulf

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MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data. Description

Documentation

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

Important Notes

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

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 --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 ~]$

Batch job

Most jobs should be run as batch jobs.

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

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. 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

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 mixcr`	Loads the mixcr module for each subjob in the swarm