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d-wdj opened this issue Mar 13, 2025 · 0 comments
Open

Unable to stage file from S3 in AWS Thailand region #5884

d-wdj opened this issue Mar 13, 2025 · 0 comments

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@d-wdj
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d-wdj commented Mar 13, 2025

Bug report

AWS Thailand region (ap-southeast-7) is new and thus as per the deprecation announcement will not be supported by the Java SDK v1. This leads to my pipeline not being able to localise any file from any AWS S3 bucket in the region.
AWS Key/secret confirmed to be correct as I have a different service working just fine as it is on the Java v2 SDK.

Expected behavior and actual behavior

Expected: staging file from S3 in Thailand region should work seamlessly.
Actual: getting 'The provided token is malformed or otherwise invalid' error message.

Steps to reproduce the problem

#!/usr/bin/env nextflow

process TestProcess {
    container 'some-container'
    pod ImagePullSecrets: 'some-ecr-key'
    
    cpus 1
    memory '500 MB'

    input:
    path test_file
 
    output:
    path 'head.txt'
 
    script:
    """
    head -n 15 ${test_file} > head.txt
    """
}

workflow {
    TestProcess(params.test_file)
}

Where params.text_file is a S3 file path of a bucket in the Thai (ap-southeast-7) region.

Program output

Nextflow 25.01.0-edge is available - Please consider updating your version to it
N E X T F L O W  ~  version 24.09.2-edge
Launching `/run/main.nf` [nf-74226e9a126e412fa027b0d498fcb60a] DSL2 - revision: 857f361c6f
Downloading plugin [email protected]
Downloading plugin [email protected]
WARN: Unable to get file attributes file: s3://<bucket in ap-southeast-7 region>/1kg_dummy_demographics.tsv -- Cause: com.amazonaws.services.s3.model.AmazonS3Exception: The provided token is malformed or otherwise invalid. (Service: Amazon S3; Status Code: 400; Error Code: InvalidToken; Request ID: J0WKMR4C4RK7Q6E6; S3 Extended Request ID: OooULRIiHfycLjJFsw3gI6FrDFZMZFqoroO1ppLCjVLZNXjY+wYzSySfjCsmm/jI9pkAtI1G0oGQLR70smmn1ffs6SAHRtyr; Proxy: null), S3 Extended Request ID: OooULRIiHfycLjJFsw3gI6FrDFZMZFqoroO1ppLCjVLZNXjY+wYzSySfjCsmm/jI9pkAtI1G0oGQLR70smmn1ffs6SAHRtyr
ERROR ~ Error executing process > 'TestProcess'

Caused by:
  The provided token is malformed or otherwise invalid. (Service: Amazon S3; Status Code: 400; Error Code: InvalidToken; Request ID: J0WMGGX6ERYXJH2Z; S3 Extended Request ID: 9jNwy7gtGryj4L/39MEbUzew6CvPvG8I4FIUm/CF26L2KtBKQuZ2EWJp7klTRn+ToHToIac4ojMw6HqILltKxp0BLL3w54Zz; Proxy: null)



 -- Check '.nextflow.log' file for details
stream closed EOF for namespace/nf-74226e9a126e412fa027b0d498fcb60a (nf-74226e9a126e412fa027b0d498fcb60a)

Environment

  • Nextflow version: v24.0
  • EKS

Additional context

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