Mixcr on Biowulf
Documentation
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 mixcrwhere
-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 |