`Error: net/http: TLS handshake timeout`

[michtrofimov]

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?

[mtntsuchiya]

Dear @michtrofimov ,

Thank you for reporting this issue. I was not able to replicate it (either from inside or outside our network). I'll pass down the information to our developers and they will take a look at it.

I'll keep you posted when a fix is available.

Thanks again.
Best,
Mirian