dbGAP retrieve issue

[prete]

Summary

I've got dbGAP access to samples. When I used prefetch to get them I got a "Failed to resolve" issue. After that, when I try to retrieve them using Data Locator API, I get links to a bucket which I don't have access for.

I would expect either prefetch working or the API returning working links (but these ones don't seem to have a signature).

Could you please advise?

Steps

Using prefetch

Got sratoolkit v3.2.0 from the prebuilt binaries, use prefetch as per the instructions here:

prefetch --ngc my_file.ngc SRR29291742

I got

2025-01-17T11:49:40 prefetch.3.2.0: 1) Resolving 'SRR29291742'...
2025-01-17T11:49:43 prefetch.3.2.0 err: name not found while resolving query within virtual file system module - failed to resolve accession 'SRR29291742' - no data ( 404 ); ncbi_phid='D0BD4004F39DCE55000048B262D88C98.1.m_2'
2025-01-17T11:49:43 prefetch.3.2.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores
2025-01-17T11:49:43 prefetch.3.2.0: 1) Failed to resolve 'SRR29291742'...

Using Data Locator API

Query the SRA Data Locator v2 API with the following command:

curl -s -X POST -F ngc="@my_file.ngc" "https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR29291742"

Result from that endpoint is (partialy redacted)

{
  "version": "2",
  "result": [
    {
      "bundle": "SRR29291742",
      "status": 200,
      "msg": "ok",
      "files": [
        {
          "object": "remote|186245925",
          "accession": "SRR29291742",
          "type": "fastq",
          "name": "XXXX_L001_I1_001.fastq.gz",
          "size": 125161333,
          "md5": "aff316915995185719d0a3360a0ba497",
          "modificationDate": "2024-06-18T04:50:22Z",
          "locations": [
            {
              "service": "s3",
              "region": "us-east-1",
              "link": "https://s3.amazonaws.com/cds-xxx-phsNNNNNN/XXXX_L001_I1_001.fastq.gz"
            }
          ]}
      ]}
  ]}

locations doesn't have "expirationDate " and link is not signed.

[klymenko]

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