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Purpose of this guide
This guide is designed to step you though running the anacapa toolkit on QUTs HPC, as the published anacapa documentation on Github can be a bit hard to follow and needs some modification to work on the HPC.
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https://www.youtube.com/watch?v=s3ii48qYBxA
Step 1: initial setup
You will be running various processes on the HPC that require quite a lot of processing power. Do not run these command on the 'head node' (which is the node you enter when you log on). Instead, either submit these command via a PBS script or an interactive PBS session, which runs your processes on another node.
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This request gets put in the HPC queue until there is an available node with sufficient resources. This may take several minutes, or possibly longer.
Create your working directory
From your home directory, create a subdirectory called ‘anacapa’ ‘anacapa’ and enter this subdirectory. This guide has commands that assume your
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cd ~
mkdir anacapa
cd anacapa |
Create a directory for your fastq files and move them there
The fastq directory should be created in your anacapa directory.
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mkdir ~/anacapa/fastq |
Move your fastq files to this directory. Your fastq files will need to be uploaded to the HPC first. To copy them from a Windows PC to the HPC, you can use a tool like WinSCP: https://winscp.net/eng/index.php
You can either copy them from your local PC, directly to the fastq directory you created (using something like WinSCP) or if they are already on the HPC but in a different directory, move to that directory ('cd ~/directory_where_fastq_files_are') then copy them across to the anacapa/fastq directory you created:
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cp *.fastq.gz ~/anacapa/fastq |
*NOTE: the above command assumes your fastq files have the ‘.fastq.gz’ suffix, which is the most common. But they may be uncompressed (i.e. just ‘samplename.fastq’) or something like samplename.fq.gz, in which case you’d change the above to 'cp *.fq.gz ~/anacapa/fastq'
Step 2: Running anacapa on Singularity
Anacapa uses many tools, which would be difficult and time consuming to install all of them on the HPC. Fortunately, the developers of Anacapa have created a Singularity image that contains all the required tools. Once the image is downloaded, all the standard tools and commands in the Anacapa guide can be run by prefixing them with ‘singularity exec anacapa-1.5.0.img’ which runs the subsequent command in the singularity container.
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Download the Anacapa Singularity container to your anacapa directory.
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cd ~/anacapa
wget https://zenodo.org/record/2602180/files/anacapa-1.5.0.img |
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