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Pear on Biowulf & Helix

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.

Running on Helix

$ module load pear
$ cd /data/$USER/dir
$ pear -f forward.fq -r reverse.fq -o outfile

Running a single batch job on Biowulf

1. Create a script file similar to the lines below.

#!/bin/bash

module load pear
cd /data/$USER/dir
pear -f forward.fq -r reverse.fq -o outfile

2. Submit the script on biowulf:

$ sbatch jobscript

For more memory requirement (default 4gb), use --mem flag:

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; pear -f forward.fq -r reverse.fq -o outfile
  cd /data/$USER/dir2; pear -f forward.fq -r reverse.fq -o outfile
  cd /data/$USER/dir3; pear -f forward.fq -r reverse.fq -o outfile
	[......]
  

Submit the swarm file:

  $ swarm -f swarmfile --module pear

-f: specify the swarmfile name
--module: set environmental variables for each command line in the file

To allocate more memory, use -g flag:

  $ swarm -f swarmfile -g 10 --module pear

-g: allocate more memory

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. 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.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load pear
cn999$ cd /data/$USER/dir
cn999$ pear -f forward.fq -r reverse.fq -o outfile

cn999$ exit
exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem flag. For example

biowulf$ sinteractive --mem=10g

Documentation

http://sco.h-its.org/exelixis/web/software/pear/