# RESCRIPt 'get-ncbi-genomes' and 'get-ncbi-data-protein' functions not supported?
**URL:** https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995
**Category:** Technical Support
**Tags:** rescript
**Created:** [February 18, 2026, 4:41pm UTC](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995 "2026-02-18T16:41:38Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@Adam\_Cantor](https://forum.qiime2.org/u/Adam_Cantor)
#### Post date: [February 18, 2026, 4:41pm UTC](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995/1 "2026-02-18T16:41:38Z")
Was trying the RESCRIPt ‘get-ncbi-genomes’ function in a q2 v2025.4 environment on my HPC. For context, just running Entrez queries works fine. My test command: `qiime rescript get-ncbi-genomes --p-taxon "Bifidobacterium breve" --verbose --output-dir bifido_genomes_test`
And got:
> Unexpected error while calling NCBI Datasets API: (410)
> Reason: Gone
> HTTP response headers: HTTPHeaderDict({'Date': 'Wed, 18 Feb 2026 14:54:10 GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains; preload', 'Content-Security-Policy': 'upgrade-insecure-requests', 'Ncbi-Phid': '1D32EE4EE6A5920500002AB74706E8F4.1', 'Content-Type': 'application/json', 'Content-Length': '333', 'X-Datasets-Version': '18.17.1', 'Vary': 'Accept-Encoding', 'X-UA-Compatible': 'IE=Edge', 'X-XSS-Protection': '1; mode=block'})
> HTTP response body: {"error": "This version of the API has been retired ( [Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools - NCBI Insights](https://ncbiinsights.ncbi.nlm.nih.gov/2024/02/20/updates-ncbi-datasets-apis-command-line-tools) ). Please migrate to the latest version to continue using our services. For more information, visit our API documentation at [NCBI Datasets v2 REST API](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/api/rest-api/) "}
I then found that the 'get-ncbi-protein-data' function does not have the same issue, but instead when I ran: `qiime rescript get-ncbi-data-protein --p-query "G1p2" --p-logging-level DEBUG --verbose --output-dir "ncbi_protein_test"`
I get a repeating cycle of:
> INFO:2026-02-18 10:18:25,731:MainProcess:Downloading 31 sequences
> DEBUG:2026-02-18 10:18:33,770:LokyProcess-2:request lock acquired
> DEBUG:2026-02-18 10:18:34,171:LokyProcess-2:request lock released
> DEBUG:2026-02-18 10:18:34,171:LokyProcess-2:Request failed with code 400. This could be because all of the requested accession ids are invalid, or it could just be a temporary failure. Retrying.
> DEBUG:2026-02-18 10:18:36,176:LokyProcess-2:request lock acquired
> DEBUG:2026-02-18 10:18:36,575:LokyProcess-2:request lock released
> DEBUG:2026-02-18 10:18:36,575:LokyProcess-2:Request failed with code 429. Retrying.
> DEBUG:2026-02-18 10:18:40,579:LokyProcess-2:request lock acquired
> DEBUG:2026-02-18 10:18:40,982:LokyProcess-2:request lock released
> DEBUG:2026-02-18 10:18:40,982:LokyProcess-2:Request failed with code 400. This could be because all of the requested accession ids are invalid, or it could just be a temporary failure. Retrying.
etc, etc. seemingly randomly between code 429 and code 400.
Also tried increasing # of cores, and making the query 'G1p2[prot]', with no change.
But finally, using the main 'get-ncbi-data' function with similar queries **does** work, so with command: `qiime rescript get-ncbi-data --p-query "Bifidobacterium breve[or] OR G1p2[prot]" --output-dir ncbi_data_test --p-logging-level DEBUG --verbose --p-n-jobs 8` it finds ~75k sequences and downloads them as expected.
So the questions are:
1. Why are 'get-ncbi-genomes' and 'get-ncbi-data-proteins' failing? Have they been silently deprecated?
2. Why are they failing **differently**? Specifically, how come 'get-ncbi-genomes' seems to be using an outdated API?
If this is just a versioning or weird dependency issue, that's fine of course, and if this was more of an immediate problem I'd probably next try reinstalling the same version of rescript with a minimal q2 environment, and then try installing the latest version. But I didn't see any discussion about this anywhere, so I'd be interested to hear any insights.
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### Author:  [@misialq](https://forum.qiime2.org/u/misialq)
#### Post date: [February 19, 2026, 11:40am UTC](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995/5 "2026-02-19T11:40:46Z")
Hey @Adam_Cantor,
Thanks for reaching out! I am not sure whether the two issues you encountered are necessarily related to one another but here's what's going on:
1. `get-ncbi-genomes`: the API was indeed deprecated; we did update RESCRIPt to reflect that change - if you use our latest distributions (2026.1) this action should work correctly.
2. `get-ncbi-data-protein`: there was an issue in how we were constructing the query to NCBI which resulted in the behaviour you observed. I'm not sure why this exactly happened now - I suspect that NCBI must have updated something here as well (this is a different API than the one used by the genome-fetching action). We have a fix which should soon be merged - it will be included in the 2026.4 release.
It sounds to me like you were able to download what you needed for now, is that correct?
Cheers,
Michal
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### Author:  [@Adam\_Cantor](https://forum.qiime2.org/u/Adam_Cantor)
#### Post date: [February 19, 2026, 4:47pm UTC](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995/6 "2026-02-19T16:47:30Z")
Hi Michal,
Yes, was able to get what I needed. Just wanted to be sure this wasn't a larger issue. Thanks for your response and glad to hear it works in the latest version.
Adam
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 22, 2026, 10:47pm UTC](https://forum.qiime2.org/t/rescript-get-ncbi-genomes-and-get-ncbi-data-protein-functions-not-supported/33995/7 "2026-03-22T22:47:39Z")
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