chopper on Biowulf

Filtering and trimming for long-read sequencing data (PacBio/ONT). Filtering is done on average read quality and minimal or maximal read length, and applying a headcrop (start of read) and tailcrop (end of read) while printing the reads passing the filter.

Important Notes

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
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 chopper
[user@cn3144 ~]$ chopper --threads 2 -q 10 -l 500 < $CHOPPER_HOME/test/test.fastq | gzip > filtered.fastq.gz
Kept 205 reads out of 250 reads
[user@cn3144 ~]$ 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. For example:

set -e
module load chopper
chopper -q 10 -l 500 < $CHOPPER_HOME/test/test.fastq | gzip > filtered.fastq.gz

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
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. chopper.swarm). For example:

gunzip -c sample1.fq.gz | chopper -q 10 -l 500 | gzip > sample1.filtered.fq.gz
gunzip -c sample2.fq.gz | chopper -q 10 -l 500 | gzip > sample2.filtered.fq.gz
gunzip -c sample3.fq.gz | chopper -q 10 -l 500 | gzip > sample3.filtered.fq.gz
gunzip -c sample4.fq.gz | chopper -q 10 -l 500 | gzip > sample4.filtered.fq.gz

Submit this job using the swarm command.

swarm -f chopper.swarm [-g #] [-t #] --module chopper
-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 chopper Loads the chopper module for each subjob in the swarm