Essential container in task exited - AWS Batch Dashboard

[DivyaThottappilly]

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Trying to set up a genomics workflow with AWS backend References : https://aws.amazon.com/blogs/compute/using-cromwell-with-aws-batch/ https://cromwell.readthedocs.io/en/stable/tutorials/AwsBatch101/

   AWS 
  java -Dconfig.file=aws-cromwell-batch.conf -jar cromwell-75.jar run hello.wdl -i hello.inputs

Cromwell-Error.docx

java -Dconfig.file=aws-cromwell-batch.conf -jar cromwell-75.jar run hello.wdl -i hello.inputs

include required(classpath("application"))

aws {

application-name = "cromwell" auths = [ { name = "default" scheme = "default" } ] region = "us-east-1" } engine { filesystems { s3.auth = "default" } } call-caching { enabled = true invalidate-bad-cache-results = true } docker { hash-lookup { enabled = false # How should docker hashes be looked up. Possible values are "local" and "remote" # "local": Lookup hashes on the local docker daemon using the cli # "remote": Lookup hashes on docker hub and gcr method = "remote" } }

backend { default = "AWSBATCH" providers { AWSBATCH { actor-factory = "cromwell.backend.impl.aws.AwsBatchBackendLifecycleActorFactory" config { numSubmitAttempts = 10 numCreateDefinitionAttempts = 10 concurrent-job-limit = 1000 root = "s3://cromwell-aws-hello/cromwell-execution" auth = "default" default-runtime-attributes { queueArn = "arn:aws:batch:us-east-1:XXXXXXXXX:job-queue/python-batch" , scriptBucketName = "cromwell-aws-hello" } filesystems { s3 { auth = "default" } } # Emit a warning if jobs last longer than this amount of time. This might indicate that something got stuck in the cloud. slow-job-warning-time: 24 hours } } } }

Cromwell-Error.docx config file.docx

How to give Timeout options for Job definitions?

[DeltaCircuit]

Hey @DivyaThottappilly do you still have this issue? I'm trying to get up and running a basic Hello World but keeps getting an S3Exception null error (301).

It seems like you've already past that stage and if you don't mind, could you help me setup this?

[DivyaThottappilly]

Issue was resolved and issue was due to launch template of EC2 and It should be launched with ssm agent installed on it . Better option is to use Amazon genomics cli . When you deploy a Context agc will create batch queues and s3 for you . It's better to use that queue and s3 in cromwell cofig . It works better.

Regards, Divya

On Fri, Apr 8, 2022 at 3:13 AM thousand-petalled @.***> wrote:

Hey @DivyaThottappilly https://github.com/DivyaThottappilly do you still have this issue? I'm trying to get up and running a basic Hello World but keeps getting an S3Exception null error (301).

It seems like you've already past that stage and if you don't mind, could you help me setup this?

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/cromwell/issues/6671#issuecomment-1092523379, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGA4NTQVWHYKZC7RLKGT4OTVD7MCNANCNFSM5N3DE7QQ . You are receiving this because you were mentioned.Message ID: @.***>