Hi all, I'm running the pipeline for the first tim...
# methylseqy
yokofakun
11/20/2025, 2:36 PMHi all, I'm running the pipeline for the first time. I got the following error:
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WARN: Unable to get file attributes file: <s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa> -- Cause: software.amazon.awssdk.services.s3.model.S3Exception: (Service: S3, Status Code: 403, Request ID: null) (SDK Attempt Count: 1)
WARN: Unable to get file attributes file: <s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex> -- Cause: software.amazon.awssdk.services.s3.model.S3Exception: (Service: S3, Status Code: 403, Request ID: null) (SDK Attempt Count: 1)👀 1
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Maxime Garcia
11/20/2025, 2:54 PMthe files do exist, so I'm guessing more a problem with an anonymous access to it
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yokofakun
11/20/2025, 2:56 PM@Maxime Garcia I'm not sure I understand. Is there anything I can do on my side (proxy... ) ?
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Maxime Garcia
11/20/2025, 2:56 PMyou can run rnaseq or sarek on your side?
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yokofakun
11/20/2025, 3:33 PM@Maxime Garcia same error for Sarek:
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WARN: Unable to get file attributes file: <s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta> -- Cause: software.amazon.awssdk.services.s3.model.S3Exception: (Service: S3, Status Code: 403, Request ID: null) (SDK Attempt Count: 1)
WARN: Unable to get file attributes file: <s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz> -- Cause: software.amazon.awssdk.services.s3.model.S3Exception: (Service: S3, Status Code: 403, Request ID: null) (SDK Attempt Count: 1)
ERROR ~ (Service: S3, Status Code: 403, Request ID: null) (SDK Attempt Count: 1)m
Maxime Garcia
11/20/2025, 3:42 PMYeah. I would recommend downloading the data beforehand and using the igenomes_base to point to the right direction
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yokofakun
11/20/2025, 3:45 PM@Maxime Garcia ok merci/thanks
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Phil Ewels
11/20/2025, 11:26 PMI think this is the thing where you need no-sign-request to access the public data in s3 iGenomes
Phil Ewels
11/20/2025, 11:26 PMAnd if you have your own AWS credentials set up, that's effectively impossible
Phil Ewels
11/20/2025, 11:26 PMSo it tries to authenticate to the iGenomes bucket with your credentials, which fails
Phil Ewels
11/20/2025, 11:26 PMAs @Maxime Garcia says, the easy fix is to make a copy of the reference data 😕
Phil Ewels
11/20/2025, 11:27 PMI still hope for a longer-term fix at some point. We were discussing it not long ago in the Nextflow team.
Phil Ewels
11/20/2025, 11:27 PMIf you're using Seqera / Fusion, I guess you should be able to mount the iGenomes bucket and then point to that as a local path. That's probably fine, and avoids the copying step..
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Maxime Garcia
11/21/2025, 6:59 AMIf I remember well, the issue Pierre is facing is that he's running on a machine behind a proxy
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yokofakun
11/24/2025, 12:25 PMupdate: yes, that was the proxy.
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