Description
The Illumina DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform provides accurate, ultra-rapid secondary genomic analysis of sequencing data.
Please do not use DRAGEN for standard calculation. We strongly recommend you to read the DRAGEN documentation before submitting a job, to understand what jobs and workflows can profit from running on DRAGEN.
Dragen is a dedicated resource. If you want to run jobs on DRAGEN please send a mail to tsd-drift@usit.uio.no.
Home page
https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html
Documentation
More information about running DRAGEN jobs can be found in the manufacturers' user documentation and the best practices guide(PDF).
Usage
Users should use Dragen by using a standard job script, except:
Modify the --account to include _dragen:
#SBATCH --account=pXX_dragen
PATH=$PATH:/opt/edico/bin/
Important:
- Only one job can run on DRAGEN at a time. A job will get exclusive access to all CPUs and RAM on the node. If there is a job running, all other submitted jobs will be in pending (PD) state until the running job terminates.
- When a job requesting cores is submitted (e.g. #SBATCH -c 6) pending jobs will report (ReqNodeNotAvail, UnavailableNodes:dragen-2).
- $HOME (/tsd/pXX/home) is automatically mounted on the DRAGEN node.
- Jobs can be submitted from $HOME or from /cluster/projects/pXX. Do not perform calculations (file I/O) in $HOME. I/O heavy jobs should use $SCRATCH, the local /staging/projects/pXX or /cluster/projects/pXX.
- $SCRATCH will be automatically deleted after the execution of the job, but the local /staging/projects/pXX disk is not, and it is the responsibility of the users to clean it after the job has been successfully executed. Do not store data here permanently.
- If you get error messages about common commands not being found, this is due to bin (or less likely, sbin) missing from $PATH. This happens because jobs inherit their environment from the shell running sbatch. This can be solved by either adding it to the $PATH of the shell running sbatch, or by adding it to your job script.
Nodes
There are currently 2 Dragen nodes in Colossus and both run version 4.0.3. To select a specific node, add the following line to your script:
#SBATCH --nodelist=dragen-3
Software
Software modules are not currently available on DRAGEN. Software may be installed upon request. DRAGEN commands work as normal.
Accounting
Accounting is set up so that a job on DRAGEN is accounted for 28 PEs (i.e. the number of CPUs on the machine). This means that you will be charged as you were running on a normal node using all available 28 CPUs.
Call us
Opening hours are weekdays from 08:30 to 17:00 and Saturdays from 10:00 to 15:00.
Phone number: 22 84 00 04
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Students and employees can book a Zoom meeting with UiO Helpdesk. Available hours are Tuesday to Thursday between 11:00 and 13:00.
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