ncbi / ncbi/datasets

`Error: net/http: TLS handshake timeout`

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Description

Describe the bug
I am trying to download taxon Escherichia on my HPC and get an error TLS handshake timeout. This error was already mentioned by two people in other issue https://github.com/ncbi/datasets/issues/509.

Command:

datasets download genome taxon 561 --dehydrated

Output:

Error: Post "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon_suggest": POST https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon_suggest giving up after 1 attempt(s): Post "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon_suggest": net/http: TLS handshake timeout

Use datasets download genome taxon <command> --help for detailed help about a command.

Debug output of datasets is next:

datasets download genome taxon 561 --dehydrated --debug
2026/03/17 10:49:09
POST /datasets/v2/taxonomy/taxon_suggest HTTP/1.1
Host: api.ncbi.nlm.nih.gov
User-Agent: OpenAPI-Generator/1.0.0/go
Content-Length: 129
Accept: application/json
Content-Type: application/json
Ncbi-Phid: D9A1C8F516AB1F5EE08CFEB4
X-Datasets-Client: datasets-cli
X-Datasets-Client-Arch: amd64
X-Datasets-Client-Cmd: download genome taxon 561 --dehydrated --debug
X-Datasets-Client-Os: linux
X-Datasets-Client-Version: 18.21.0
Accept-Encoding: gzip

{"exact_match":true,"tax_rank_filter":"higher_taxon","taxon_query":"561","taxon_resource_filter":"TAXON_RESOURCE_FILTER_GENOME"}

Error: Post "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon_suggest": POST https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon_suggest giving up after 1 attempt(s): Post "https://api.ncbi.nlm.nih.gov/datasets/v2/taxonomy/taxon_suggest": net/http: TLS handshake timeout

Use datasets download genome taxon <command> --help for detailed help about a command.

And suggested debug of API with curl is next

curl -X POST "https://api.ncbi.nlm.nih.gov/datasets/v2/genome/dataset_report"  -H 'accept: application/json' -H 'content-type: application/json'  -d '{"accessions":["GCF_000005845"],"returned_content":"ASSM_ACC"}'
{"reports":[{"accession":"GCF_000005845.2","source_database":"SOURCE_DATABASE_REFSEQ"}],"content_type":"ASSM_ACC","total_count":1}

Indicate what operating system you're using
Description: Ubuntu 22.04.5 LTS Jammy
datasets version: 18.21.0

Question
I believe this issue is frequent among users. And in previous topic its been mentioned that the problem comes from client network configuration. Can you suggest with which request I should come to my system administrator?

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing datasets download genome taxon 561 --dehydrated --debug on Ubuntu 22.04.5 with datasets 18.21.0, then compare the failing taxonomy/taxon_suggest request with the successful genome/dataset_report curl request. Done means identifying whether the report supports a client or system-network fix and documenting the administrator request.

Written by the indexing model from the issue text.

Assessment

Tech stack
go, ubuntu
Domain
cli, networking
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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