Resources fail to be created during batch-genomics-pipeline execution

[ury]

Hi, batch-genomics-pipeline fails with the following error:

Embedded stack arn:aws:cloudformation:us-west-1:xxxxxxxxxxx:stack/batch-genomics-pipeline-RoleStack-xxxxxxxxxxxxx/xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxx was not successfully created: The following resource(s) failed to create: [BatchServiceRole, SpotFleetRole, ECSInstanceRole, ECSTaskRole, StatesExecutionRole].

I don't see any further details. Did I miss a step? Any advice?

Thanks, Ury

[ury]

One problem found: the role template is using the deprecated policy "AmazonEC2SpotFleetRole" instead of the updated "AmazonEC2SpotFleetTaggingRole". Unfortunately, after fixing this, the stack still fails with the same error. I will continue investigating

[ury]

VPCStack fails with the following message:

Embedded stack arn:aws:cloudformation:us-west-1:xxxxxxxxxxx:stack/batch-genomics-pipeline-VPCStack-xxxxxxxxxxxx/xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxx was not successfully created: The following resource(s) failed to create: [RouteTable, SubnetB, SubnetC, SecurityGroup].

[rulaszek]

Hello Ury,

We will be deprecating this solution shorty for a new solution for secondary analysis. Would you be interested in beta testing? It will resolve this issue and get you end to end in minutes with a secondary analysis solution with full CI/CD - repos and deployment pipeline. If you are interested send me an email at rulaszek@amazon.com and I will send you a link. I will try to find some time later this week to look into this issue.

[ury]

Thank you for your response. With the help of taskcat, it looks like the number of subnets (in us-west-1) is the cause of this error. I've removed subnets B and C and I'm no longer getting the above error. Unfortunately (once again...), the script fails on the tool stack - this time without showing any error, neither in the Linux terminal nor in the CloudFormation console (which shows all stacks as "succeeded". The new solution sounds very interesting. I will contact you as you specified.

[sachalau]

Hello,

I'm trying to follow the tutorial too and I'm running into an error when importing the state machine into CloudFormation, that the ressources are AWS::IAM::Policy and AWS::StepFunctions::StateMachine are not supported for resource import.

I replaced AWS::IAM::Policy by AWS::IAM::ManagedPolicy because I assume it was renamed however I'm not sure with what to replace the StepFunctions.

[rulaszek]

Hello,

The AWS Solution is now GA:

https://aws.amazon.com/solutions/implementations/genomics-secondary-analysis-using-aws-step-functions-and-aws-batch/

[sachalau]

That's awesome thank you very much