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1. A HPC account

2. Nextflow installed on the HPC

3. PuTTy installed on your local computer

4. Access your HPC home directory from your PC

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If you haven’t installed Nextflow, follow the instructions in this link: Installing Nextflow

You’ll need PuTTY 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: lyra.qut.edu.au and then click ‘open’.

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Setup Windows File Explorer to access your HPC home account. Follow the instructions here:

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In session 2 and 3 (variant calling) we submitted jobs to the HPC via a PBS script. This is useful for large datasets that require lots of processing time or resources. For smaller datasets (like 16S amplicon sequence data), you can start ‘interactive mode’ on the HPC, which allocates you a temporary node with RAM/CPUs you request.

Open PuTTy and paste the text below into the command prompt:

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NOTE: I’ve selected 16 CPUs and 64gb 128gb of memory. This is based on testing of the Nextflow workflows we’ll be using and their CPU/memory requirements.

Additional interactive job for running Nanopore analysis (may start quicker as fewer resources)

qsub -I -S /bin/bash -l walltime=4:00:00 -l select=1:ncpus=5:mem=12gb

Create working directories

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Then save the file by typing <ctrl> o, press Enter, and then <ctrl> x to exit Nano.

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Copy the Illumina and Nanopore fastq files to their respective workshop directories like so:

cd $HOME
cd meta_workshop
cp /work/training/metagenomics/public_data/Illumina*.fastq.gz illumina/fastq
cp /work/training/metagenomics/public_data/Nanopore*.fastq.gz nanopore/fastq

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