Flanker is a tool for studying the homology of gene-flanking sequences. It will annotate FASTA/multi-FASTA files for specified genes, then write the flanking sequences to new FASTA files. There is also an optional step to cluster the flanks by sequence identity.

References:

• Blow J. Flanker: a tool for comparative genomics of gene flanking regions. Microbial Genomics. 2021 J Mol Biol. 2012 Jan 13;415(2):406-18.

• Documentation

• Module Name: flanker
• Multithreaded/singlethreaded/MPI...
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • TEMPLATE_HOME
• Example files in ???
• Reference data in /fdb/TEMPLATE/

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 flanker

[user@cn3144 ~]$  flanker -h

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. TEMPLATE.sh). For example:

#!/bin/bash
set -e
module load flanker
flanker < TEMPLATE.in > TEMPLATE.out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.sh

Create a swarmfile (e.g. TEMPLATE.swarm). For example:

TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out
TEMPLATE < TEMPLATE.in > TEMPLATE.out

Submit this job using the swarm command.

swarm -f TEMPLATE.swarm [-g #] [-t #] --module TEMPLATE