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Hello, I'm trying to run a Nextflow workflow with AWS Batch, but all my jobs fail with the following error:
The workflow is a small test example from a Swiss Institute of Bionformatics course, with code on GitHub here. I'm running it with the command In the container section of the job details page, the user value is
I believe this line is supposed to avoid having Docker run as root, though if I remove the line completely my jobs never get past the "Runnable" state in AWS Batch. I would greatly appreciate any insight into how to solve this error! |
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Replies: 2 comments
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I think you have to escape the dollar signs: |
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It turns out that the EC2 instance role we were using had limited permissions to S3. Changing those permissions allowed us to run a similar workflow without changing the aforementioned line. Posting in case this helps anyone in the future! |
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It turns out that the EC2 instance role we were using had limited permissions to S3. Changing those permissions allowed us to run a similar workflow without changing the aforementioned line. Posting in case this helps anyone in the future!