Overview
To be able to run these exercises, you’ll need:
A HPC account
Nextflow installed on the HPC
PuTTy installed on your local computer
Access your HPC home directory from your PC
Instructions for getting a HPC account are here: https://qutvirtual4.qut.edu.au/group/staff/research/conducting/facilities/advanced-research-computing-storage/supercomputing/getting-started-with-hpc
If you haven’t installed Nextflow, follow the instructions in this link: 25S1W1 - 1. Getting started with Nextflow
You’ll need a Terminal (Mac Users) or PuTTY (Windows users) on your PC to access the HPC.
You can download PuTTY from here: https://the.earth.li/~sgtatham/putty/latest/w64/putty.exe
Then add the HPC (Lyra) address: aqua.qut.edu.au and then click ‘open’.
Setup Windows File Explorer to access your HPC home account. Follow the instructions here:
Open a Terminal (Mac users) or PuTTy (Windows users) and paste the text below into the command prompt to start an Interactive Session:
qsub -I -S /bin/bash -l walltime=4:00:00 -l select=1:ncpus=4:mem=8gb |
It should take less than a minute for the interactive session. The interactive session will allow
We’ll be analysing Illumina amplicon data, so first we need to create the workshop directories in your home drive on the HPC. Copy and paste the following into PuTTy or Terminal:
To make sure you are in your home directory, run the following command:
cd $HOME |
Next, let’s create working folders for today's exercises:
mkdir -p $HOME/workshop/2025/S1W1/metagenomics/scripts mkdir -p $HOME/workshop/2025/S1W1/metagenomics/runs mkdir -p $HOME/workshop/2025/S1W1/metagenomics/runs/run1_test mkdir -p $HOME/workshop/2025/S1W1/metagenomics/runs/run2_ampliseq mkdir -p $HOME/workshop/2025/S1W1/metagenomics/data/illumina mkdir -p $HOME/workshop/2025/S1W1/metagenomics/data/mydata cd $HOME/workshop/2025/S1W1/metagenomics |
Let’s now copy the scripts for today’s workshop:
cp /work/training/2025/S1W1/session3_metagenomics/scripts/* $HOME/workshop/2025/S1W1/metagenomics/scripts |
Check the list of scripts:
ls -l $HOME/workshop/2025/S1W1/metagenomics/scripts |
├── create_samplesheet_nfcore_ampliseq.py ├── launch_nfcore_ampliseq_illumina.pbs ├── launch_nfcore_ampliseq_test.pbs └── samplesheet.tsv |
Now let’s copy previously downloaded Illumina amplicon data:
cp /work/training/2025/S1W1/session3_metagenomics/data/illumina/* $HOME/workshop/2025/S1W1/metagenomics/data/illumina |
This can take a couple of minutes. To check that you have copied the data you can do the following:
ls $HOME/workshop/2025/S1W1/metagenomics/data/illumina |
create_samplesheet_nfcore_ampliseq.py* Illumina24.fastq.gz Illumina39.fastq.gz Illumina53.fastq.gz Illumina10.fastq.gz Illumina25.fastq.gz Illumina3.fastq.gz Illumina54.fastq.gz Illumina11.fastq.gz Illumina26.fastq.gz Illumina40.fastq.gz Illumina55.fastq.gz Illumina12.fastq.gz Illumina27.fastq.gz Illumina41.fastq.gz Illumina56.fastq.gz Illumina13.fastq.gz Illumina28.fastq.gz Illumina42.fastq.gz Illumina57.fastq.gz Illumina14.fastq.gz Illumina29.fastq.gz Illumina43.fastq.gz Illumina58.fastq.gz Illumina15.fastq.gz Illumina2.fastq.gz Illumina44.fastq.gz Illumina59.fastq.gz Illumina16.fastq.gz Illumina30.fastq.gz Illumina45.fastq.gz Illumina5.fastq.gz Illumina17.fastq.gz Illumina31.fastq.gz Illumina46.fastq.gz Illumina6.fastq.gz Illumina18.fastq.gz Illumina32.fastq.gz Illumina47.fastq.gz Illumina7.fastq.gz Illumina19.fastq.gz Illumina33.fastq.gz Illumina48.fastq.gz Illumina8.fastq.gz Illumina1.fastq.gz Illumina34.fastq.gz Illumina49.fastq.gz Illumina9.fastq.gz Illumina20.fastq.gz Illumina35.fastq.gz Illumina4.fastq.gz samplesheet.tsv Illumina21.fastq.gz Illumina36.fastq.gz Illumina50.fastq.gz Illumina22.fastq.gz Illumina37.fastq.gz Illumina51.fastq.gz Illumina23.fastq.gz Illumina38.fastq.gz Illumina52.fastq.gz |
Let’s move to the data folder:
cd $HOME/workshop/2025/S1W1/metagenomics/data |
Now we are ready for the next excercise downloading public data from the European Nucleotide Archive (ENA) https://www.ebi.ac.uk/ena/browser/view/PRJEB28612
25S1W1 - 3. Download public metagenomics data from ENA