[GH-ISSUE #1928] Connecting to S3 for Thousand genomes data #972

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opened 2026-03-04 01:50:19 +03:00 by kerem · 2 comments

kerem commented

2026-03-04 01:50:19 +03:00

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Originally created by @Phillip-a-richmond on GitHub (Mar 29, 2022).
Original GitHub issue: https://github.com/s3fs-fuse/s3fs-fuse/issues/1928

Hello,

I'm trying to mount the public S3 bucket (s3:/1000genomes) to visualize these large files as a mounted filesystem using Integrative Genomics Viewer (IGV).

I installed s3fs through brew on my Mac (Mac Pro 2019, OS v10.15.7) and it seems to work fine. But when I run the mount command I get a "Device not configured" error after it hangs for a few moments. Perhaps it's the syntax of my command?

The s3 cli equivalent of viewing the data:

aws s3 ls s3://1000genomes/data/NA21143/alignment/ --no-sign-request

The command I'm running which fails:

s3fs -o public_bucket=1 s3:/1000genomes/data/NA21143/alignment/  ~/S3_Mount/

Where ~/S3_Mount/ is just an empty directory on my local machine.

Any help would be appreciated!

Thanks,
Phil

Originally created by @Phillip-a-richmond on GitHub (Mar 29, 2022). Original GitHub issue: https://github.com/s3fs-fuse/s3fs-fuse/issues/1928 Hello, I'm trying to mount the public S3 bucket (s3:/1000genomes) to visualize these large files as a mounted filesystem using Integrative Genomics Viewer (IGV). I installed s3fs through brew on my Mac (Mac Pro 2019, OS v10.15.7) and it seems to work fine. But when I run the mount command I get a "Device not configured" error after it hangs for a few moments. Perhaps it's the syntax of my command? The s3 cli equivalent of viewing the data: ``` aws s3 ls s3://1000genomes/data/NA21143/alignment/ --no-sign-request ``` The command I'm running which fails: ``` s3fs -o public_bucket=1 s3:/1000genomes/data/NA21143/alignment/ ~/S3_Mount/ ``` Where ~/S3_Mount/ is just an empty directory on my local machine. Any help would be appreciated! Thanks, Phil

kerem

2026-03-04 01:50:19 +03:00

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kerem commented

2026-03-04 01:50:20 +03:00

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@gaul commented on GitHub (Jun 12, 2022):

s3fs does not use the s3:// syntax. Please try:

s3fs -o public_bucket=1 1000genomes:/data/NA21143/alignment/ ~/S3_Mount/

Note colon after bucket name).

@gaul commented on GitHub (Jun 12, 2022): s3fs does not use the `s3://` syntax. Please try: ``` s3fs -o public_bucket=1 1000genomes:/data/NA21143/alignment/ ~/S3_Mount/ ``` Note colon after bucket name).

kerem commented

2026-03-04 01:50:20 +03:00

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@gaul commented on GitHub (Sep 8, 2023):

Please reopen if your symptoms persist.

@gaul commented on GitHub (Sep 8, 2023): Please reopen if your symptoms persist.

kerem referenced this issue

2026-03-04 02:01:55 +03:00

[PR #972] [MERGED] Add instructions for Amazon Linux #1736