q2 fondue get-ids-from-query error

[meghna_swayambhu]

Hello QIIME2 team,

I am trying to run q2 fondue and am following the tutorial: q2-fondue/README.md at main · bokulich-lab/q2-fondue · GitHub

I get an error when I run the commands and would be very grateful for assistance!

(fondue) meghnaswayambhu@Meghnas-MacBook-Pro-2 fondue_test % qiime fondue get-ids-from-query --p-query "txid410656[Organism] AND "public"[Filter] AND (chicken OR poultry)" --p-email [address hidden] --p-n-jobs 4 --o-ids run_ids.qza --verbose

2025-06-05 17:42:03,144 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "Reoos9MPQCqqRawKbSbFFQ==", "util": "elink"}}

2025-06-05 17:42:05,157 [MainThread] [INFO] [entrezpy.conduit.Conduit]: {"querying": {"queryid": "mFQWflBFSrWH__M77EujRw==", "util": "efetch"}}

2025-06-05 17:44:26,742 [MainThread] [ERROR] [entrezpy.conduit.Conduit]: {"request error": {"queryid": "mFQWflBFSrWH__M77EujRw==", "action": "abort"}}

Thank you!

Best,
Meghna

[Nicholas_Bokulich]

Hi @meghna_swayambhu ,
It's a bit of a cryptic error so I am not totally sure, but it looks like an error in the query.

I get zero results when I manually search this query at Home - SRA - NCBI

On the other hand, this query gets lots of hits: "txid410656[Organism] AND (chicken OR poultry)"

So I am not sure if the problem is that the public[Filter] query yields zero results, or if it's because the use of quotes around "public" is causing something to break. Either way, I think removing that keyword to fix your query should work!

[meghna_swayambhu]

Hi Nicholas,
Thank you very much! Removing the "public" part entirely worked!

Meghna