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cfn-ps-illumina-dragen's Introduction

quickstart-illumina-dragen

DRAGEN on the AWS Cloud

This Quick Start deploys Dynamic Read Analysis for GENomics Complete Suite (DRAGEN CS), a data analysis platform by Illumina, on the AWS Cloud in about 15 minutes.

DRAGEN CS enables ultra-rapid analysis of next-generation sequencing (NGS) data, significantly reduces the time required to analyze genomic data, and improves accuracy. It includes bioinformatics pipelines that provide highly optimized algorithms for mapping, aligning, sorting, duplicate marking, and haplotype variant calling. These pipelines include DRAGEN Germline V2, DRAGEN Somatic V2 (Tumor and Tumor/Normal), DRAGEN Virtual Long Read Detection (VLRD), DRAGEN RNA Gene Fusion, DRAGEN Joint Genotyping, and GATK Best Practices.

The Quick Start builds an AWS environment that spans two Availability Zones for high availability, and provisions two AWS Batch compute environments for Spot Instances and On-Demand Instances. These environments include DRAGEN F1 instances that are connected to field-programmable gate arrays (FPGAs) for hardware acceleration.

The Quick Start offers two deployment options:

  • Deploying DRAGEN into a new virtual private cloud (VPC) on AWS
  • Deploying DRAGEN into an existing VPC on AWS

You can also use the AWS CloudFormation templates as a starting point for your own implementation.

Quick Start architecture for DRAGEN on AWS

For architectural details, best practices, step-by-step instructions, and customization options, see the deployment guide.

To post feedback, submit feature ideas, or report bugs, use the Issues section of this GitHub repo. If you'd like to submit code for this Quick Start, please review the AWS Quick Start Contributor's Kit.

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cfn-ps-illumina-dragen's Issues

single app mode waiting to run

Hey,

When attempting to run either the somatic or germline pipeline in Dragen, the program displays a screen and remains stuck on it. Do you know how I can ı resolve this?
image

Deployment Guide error

Hey all, I am facing some issues with dragen deployment using the guide here - https://aws-ia.github.io/cfn-ps-illumina-dragen/.
I have done this before, but its been some time I and don't remember having this problem.
I just ran with "deploy in new VPC" link, here are my parameters, as seen on CloudFormation stack.

image

But I keep getting the following error

image

It looks like it fails to copy something into the bucket (or cant find source/destination?).

Since its a relatively fresh account and I didn't specify anything extra in template creation, such as IAM (I just left it empty), its strange that it fails here.

Could it be its missing from source for copying?
What direction can I take for this?

Thanks!

DRAGEN error using Deployment Guid

Hi, I am using the DRAGEN Complete Suite and using the AWS CloudStack deployment guide. When I submit a batch job, all the pre-processing steps seems to work (i.e., reference downloaded from S3 bucket, etc...) but when DRAGEN runs, it exits with the following error message:

  2024-01-09T09:54:46.188-08:00 ERROR: The following extra command line options are not recognized
  2024-01-09T09:54:46.188-08:00Copy > /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd/dragen_log_1704822886.txt 2>&1 > /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd/dragen_log_1704822886.txt 2>&1

My guess is somehow the last parameters are being passed as arguments directly to DRAGEN versus being treated as I/O pipes. Here's the command being run by the DRAGEN stack:

Executing /opt/edico/bin/dragen -f -r /ephemeral/DRAGEN/hg38/ -1 s3://XXX/temp/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz -2 s3://XXX/temp/NA24385-AJ-Son-R1-NS_S33_L001_R2_001.fastq.gz --RGID 1 --RGSM Test --enable-bam-indexing true --enable-map-align-output true --enable-sort true --output-file-prefix output --enable-map-align true --output-format BAM --output-directory /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd --enable-variant-caller true --output_status_file /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd/job-speedometer.log --intermediate-results-dir /ephemeral/ --lic-no-print > /ephemeral/9518aff5-e295-4e05-802a-f4365af3b4bd/dragen_log_1704822886.txt 2>&1

I am not sure how this is happening as I am using all the default settings. Any help would be appreciated.

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