https://github.com/multimeric/awsnextflowbug
https://github.com/multimeric/awsnextflowbug
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/multimeric/awsnextflowbug
- Owner: multimeric
- Created: 2021-09-16T06:44:58.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-03-24T10:51:02.000Z (about 3 years ago)
- Last Synced: 2025-04-02T18:15:22.284Z (12 months ago)
- Language: Nextflow
- Size: 1000 Bytes
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Nextflow AWS Bug
* First, ensure you have an AWS account configured as explained [here](https://www.nextflow.io/docs/latest/awscloud.html#)
* Then, set the queue ARN and region in the config file
* Finally, run `nextflow run bug.nf -bucket-dir some_bucket`
* After some time you should get the error: "Process `spades` terminated for an unknown reason -- Likely it has been terminated by the external system"
* At this point, run `aws batch list-jobs --job-queue MY-QUEUE-ARN --job-status FAILED --output yaml`, and when you find the job that most recently failed, it should say something like "Process `spades` terminated for an unknown reason -- Likely it has been terminated by the external system"