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PBSuite on Biowulf

The PBSuite contains two projects created for analysis of Pacific Biosciences long-read sequencing data: PBHoney and PBJelly.

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

References:

Documentation
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 sessions (user input in bold):

PBHoney

[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 pbsuite
[user@cn3144 ~]$ cp $PBSUITE_HOME/docs/honeyExample/* .
[user@cn3144 ~]$ sh workflow.sh
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

PBJelly

[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 pbsuite
[user@cn3144 ~]$ cp -r $PBSUITE_HOME/docs/jellyExample/* .
[user@cn3144 ~]$ sed -i "s|/__PATH__/_TO_/jellyExample|$PWD|g" Protocol.xml
[user@cn3144 ~]$ for stage in setup mapping support extraction assembly output
do
    Jelly.py $stage Protocol.xml
done

[user@cn3144 ~]$ summarizeAssembly.py jelly.out.fasta # check your results
[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. pbjelly.sh). For example:

#!/bin/sh
set -e
module load pbsuite

for stage in setup mapping support extraction assembly output
do
    Jelly.py $stage Protocol.xml
done

Submit this job using the Slurm sbatch command.

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

for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol1.xml || exit 1; done
for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol2.xml || exit 1; done
for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol3.xml || exit 1; done
for stage in setup mapping support extraction assembly output; do Jelly.py $stage protocol4.xml || exit 1; done

Submit this job using the swarm command.

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