StackOverflowError using AWS Batch #408
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Hi @jvivian-atreca , thanks for reporting this issue. |
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@ggabernet — Apologies, I've attached the remainder which includes the java/groovy stacktrace. I did several runs locally with the same S3 URLs and it successfully "staged" those files every time, so I'm unsure what to make of the message about file not found. I also moved those files locally and passed them in and still got the same stackoverflowerror. |
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Hi, I have the same error when running it using awsbatch profile in v1.4.2, while running it using docker profile gives me no error. Here is the script I used when running it with I suspect this is related to the awsregion being |
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Ah, yes, that could very well be, in fact I did not manage to run a pipeline in a region and stage the reference files from another region. The references are in the |
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@ggabernet Thanks! In fact, I am using the 2nd method, I have downloaded the iGenomes's data in my bucket in |
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Could you then try setting an env variable to increase the JVM resources before running the pipeline, something like: |
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@ggabernet Thanks! I tried it both on my ec2 instance in the terminal as well as adding a block like this in the nextflow.config but still have the same error. |
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I'm afraid I'm out of ideas here.... The most similar thing I could find is this: https://gitter.im/nextflow-io/nextflow/archives/2017/05/28?at=592b0233f3001cd34268cc2b But maybe you can ask in the nextflow gitter as well: https://gitter.im/nextflow-io/nextflow |
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Hi @jvivian-atreca @jiayicox1! Hope you are well. Did you find a solution to this issue? Will close for now because it seems like you have ruled out this being an issue with the pipeline and possibly related to Nextflow? Feel free to reopen if required. |
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Firstly, thank you for all the effort in putting this pipeline together.
I'm running into an issue where I can't get the workflow to execute on AWS Batch. I've tried launching it from a t2.large and t2.xlarge (16G memory) on EC2 and get the same error.
Run command
Error
The compute environments in
test-nextflow-spotare all pretty beefy and it seems to fail before it has enough time to even launch a batch node, so I don't think it's actually failing on the batch node. I'm assuming it's a config option based on nf-core/tools#446 and other examples of seeingstackoverflowerror. I've tried replacing theawsqueuewith the complete ARN and that didn't resolve it.Thanks for any help you can provide!
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