MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.
Sample session:
helix$ module load mixcr helix$ cd /data/$USER/dir helix$ mixcr align -r log.txt -t 4 \ /data/maoj/seq/ngs/2_1_62B43AAXX.192_BUSTARD-2010-11-01.fastq.gz \ /data/maoj/seq/ngs/2_2_62B43AAXX.192_BUSTARD-2010-11-01.fastq.gz \ aln.vdjca
Note the '-t' flag is required otherwise the program will occupy all available cpus on helix and crash the system.
1. Create a script file. The file will contain the lines similar to the lines below.
#! /bin/bash #SBATCH --cpus-per-task=20 #SBATCH --mail-type=BEGIN,END,FAIL module load mixcr cd /data/maoj/mixcr mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK \ /data/maoj/seq/ngs/2_1_62B43AAXX.192_BUSTARD-2010-11-01.fastq.gz \ /data/maoj/seq/ngs/2_2_62B43AAXX.192_BUSTARD-2010-11-01.fastq.gz \ aln.vdjca .... ....
2. Submit the script on Biowulf.
--cpus-per-task is a must for this program otherwise it will auto thread to all available cpus on a node
This job took 40 minutes when allocated 20 threads, 7 hours when allocated 2 threads. The input files are 4gb in size each.
see biowulf user guide for more options such as allocate more memory and longer walltime if needed.
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file:
cd /data/user/run1/; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK 1.fastq.gz 2.fastq.gz aln.vdjca cd /data/user/run2/; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK 1.fastq.gz 2.fastq.gz aln.vdjca cd /data/user/run3/; mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK 1.fastq.gz 2.fastq.gz aln.vdjca ........
The -f flag is required to specify swarm file name.
Submit the swarm job:
$ swarm -f swarmfile -t 20 --module mixcr
-t flag is a must for this program otherwise it will auto thread to all available cpus on a node.
- Use -t flag for more threads requirement (default 2 threads per line in swarmfile)
- Use --time flag for longer walltime
For more information regarding running swarm, see swarm.html
User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.
Note, --cpus-per-task is a must for the program otherwise it will auto thread to all available cpus on the node.
[user@biowulf]$ sinteractive --cpus-per-task=20
[user@pXXXX]$ cd /data/$USER/myruns
[user@pXXXX]$ module load mixcr
[user@pXXXX]$ mixcr align -r log.txt -t $SLURM_CPUS_PER_TASK 1.fastq.gz 2.fastq.gz aln.vdjca
[user@pXXXX]$ exit
slurm stepepilog here!
[user@biowulf]$
