How to install and use super-focus on deepthought

August 24, 2021

super-FOCUS

Super-FOCUS is a tool to identify the functions that the sequences in your metagenome are doing. As a benefit, it also identifies the taxonomy associated with those functions.

Super-FOCUS uses a reduced, optimized, database and fast aligners to run.

To run Super-FOCUS you need two things:

Your data, probably in fasta or fastq format
A database of things we know about. Note that this is a databse in super-FOCUS format, not in another format!

Installing Super-FOCUS on deepthought

You only need to do this step once! When you come back to deepthought you can do conda activate bioinformatics and you have super-FOCUS ready to go!

To install Super-FOCUS on deepthought we are going to use conda. Once you have conda installed, [here are more install instructions].

We start by activating our conda environment:

conda activate bioinformatics

(Note, if you great the warning: Could not find conda environment: bioinformatics, then you need to use conda create -n bioinformatics first to create the environment.)

and now we can install new software:

conda install -y -c bioconda super-focus

This will figure out all the things that need to be installed, and then install them for you. It should not take too long for the installer to complete.

Next, we need to get the databases. You can use the superfocus_downloadDB command to download them, you can download them indvidually, or if you are on deepthought you can use Rob’s version of the databases. Just set up a variable to access them like this:

If you are taking Rob’s class you can do this:

conda env config vars set SUPERFOCUS_DB=/home/edwa0468/superfocus_db/version1

NOTE: Run this command to test your diamond version:

diamond --version

If you have version v0.9.0 to v0.9.18 you need to use version 1 of the database If you have version v0.9.19 to v0.9.24 you need to use version 2 of the database If you have v0.9.25 onwards you need to use version 3 of the database

You can change the config setting above like this:

conda env config vars set SUPERFOCUS_DB=/home/edwa0468/superfocus_db/version1 conda env config vars set SUPERFOCUS_DB=/home/edwa0468/superfocus_db/version2 conda env config vars set SUPERFOCUS_DB=/home/edwa0468/superfocus_db/version3

Or you can download the databases here: diamond v1 diamond v2 diamond v3

If you use mmseqs there is only one version of the database: mmseqs

The installation is complete and now you can use it to explore your metagenomes. Next time, you can skip this section.

Using super-FOCUS on deepthought

Using Super-FOCUS in class

You can set a variable with the name of the directory:

export FQDIR=BTEC_Water

and then copy Rob’s slurm file:

cp ~edwa0468/superfocus.slurm .

and then submit that to the cluster:

sbatch superfocus.slurm

This will create a new directory called BTEC_Water.superfocus_results

Before you begin

Super-FOCUS requires that your input fastq files be in a directory. We’re going to make a directory called fastq and copy the data into there. Change barcode_01.fastq to the name of your fastq file!!

mkdir fastq
cp barcode_01.fastq fastq

(remember, the ls command will show you the files and directories that you have)

Also note:

super-focus takes quite a lot of computing resources so we are just going to run this straight on the cluster. It is bad practice to run it on the login node!

Running super-FOCUS

To run superfocus directly

Use this command

superfocus -q fastq -b ~/superfocus_db -a diamond -dir superfocus_results

To run on the cluster during class

cp ~edwa0468/superfocus.slurm ~/
sbatch ~/superfocus.slurm

We are going to make a batch file to submit the command to the cluster. Lets call our file superfocus.slurm:

nano superfocus.slurm

And then put these lines in that file

#!/bin/bash

#SBATCH --ntasks=8

superfocus --threads 8 -q fastq -b ~/superfocus_db -a diamond -dir superfocus_results

In this command:

The fastq option is the name of our input directory and is the same name we used above under Before you begin
The ~/superfocus_db option is the name of our database. If you have downloaded your own databases you should omit that information. This is the database that currently works with the version of super-FOCUS and diamond in conda
The diamond option is the aligner that we are going to run.
The superfocus_results option is where we are going to find the output

Then, we are going to submit that to run on the cluster

sbatch superfocus.slurm

and you can monitor the progress with

squeue

squeue -u <FAN>

where <FAN> is your FAN!

Notice that super-FOCUS will also output a lot of information in a file that will be called something like slurm-1709843.out (but the number will be totally different). That tells you whether the command has worked or if there was some kind of error.

Rob Edwards