mosh annotate filer-reads-pangenome error: NCBI API has been retired

[feuz (Mel)]

Dear forum

I am new to qiime2 (worked on host genomics before). I am doing the moshpit tutorial and came across an error with annotate filter-reads-pangenome (see below). Not sure how I could fix this... I am working with the latest version of moshpit.

mosh annotate filter-reads-pangenome \

--i-reads ./cache:reads_trimmed \
--o-filtered-reads ./cache:reads_filtered \
--o-reference-index ./cache:human_reference_index

Plugin error from annotate:
Unexpected error while calling NCBI Datasets API: (410)
Reason: Gone
HTTP response headers: HTTPHeaderDict({'Date': 'Thu, 13 Mar 2025 18:54:55 GMT', 'Server': 'Apache', 'Strict-Transport-Security': 'max-age=31536000; includeSubDomains; preload', 'Content-Security-Policy': 'upgrade-insecure-requests', 'Ncbi-Phid': 'D0BDA05EFBFD6485000045939A161F9E.1', 'Content-Type': 'application/json', 'Content-Length': '294', 'X-Datasets-Version': '17.1.0', '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. Please migrate to the latest version to continue using our services. For more information and migration guidance, visit our API documentation at Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools - NCBI Insights"}
.

Debug info has been saved to /tmp/qiime2-q2cli-err-4m3ol33z.log

Please guide me on what to do. Thank you very much.

[misialq (Michal Ziemski)]

Dear @feuz,

Welcome to the forum! Sorry to hear you've been experiencing issues and thanks for discovering that bug. It would seem that one of the services which we use to fetch the human genomes is not supported anymore and we will need to look into updating it. Since building the index which we are using within this action requires a few steps, in the meantime my best suggestion would be to just use the human genome to filter (GRCh37 or 38). You could use the bowtie2_build action (q2-quality-control) to build an index from the genome fasta file and then use it as input to the action you used above.

Let me know if you need more info and sorry for the trouble - we'll do our best to get this fixed soon!

Best,
Michal