`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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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