# chewBBACA DownloadSchema Schema files - organisms are mixed up **URL:** \ **Category:** usegalaxy.eu support\ **Tags:** tool-help, chewbbaca\_downloadschema\ **Created:** [April 8, 2026, 10:17am UTC](https://help.galaxyproject.org/t/chewbbaca-downloadschema-schema-files-organisms-are-mixed-up/17638 "2026-04-08T10:17:53Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Anu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/anu/32/8568_2.png) [@Anu](https://help.galaxyproject.org/u/Anu)\ **Post date:** [April 8, 2026, 10:17am UTC](https://help.galaxyproject.org/t/chewbbaca-downloadschema-schema-files-organisms-are-mixed-up/17638/1 "2026-04-08T10:17:53Z")
Hello Galaxy EU-Team and Community, I wanted to download and use the cgMLST scheme for _Listeria monocytogenes_. I selected the correct organism, but received the scheme for _Campylobacter jejuni_ instead. After checking the remaining schemes, I noticed that the first three or so appear to be correct, while the rest are either mixed up or replaced by organisms not included in the list at all. _Listeria monocytogenes_ is completely missing. As a workaround, I am downloading the scheme manually for now, but I wanted to flag this issue here in case it is an unknown problem. Best wishes, Annu ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 8, 2026, 5:36pm UTC](https://help.galaxyproject.org/t/chewbbaca-downloadschema-schema-files-organisms-are-mixed-up/17638/2 "2026-04-08T17:36:46Z")
Hi @Anu This seems pretty significant! Do you think this is in just the indexes hosted in Galaxy or a problem upstream at the tool development step? I only see one recent change that might lead to a mix up problem – overly long sequence names. These could get truncated. Please see the details here and let us know what you think! - [chewBBACA/CHANGELOG.md at master · B-UMMI/chewBBACA · GitHub](https://github.com/B-UMMI/chewBBACA/blob/master/CHANGELOG.md) You are also welcome to share you history for more specific feedback. If there is some issue with the tool wrapper, we can investigate and get it reported for a fix! 🙂 - [https://training.galaxyproject.org/training-material/faqs/galaxy/histories\_sharing.html](https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html) ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 8, 2026, 7:49pm UTC](https://help.galaxyproject.org/t/chewbbaca-downloadschema-schema-files-organisms-are-mixed-up/17638/3 "2026-04-08T19:49:22Z")
Oops, this looks indeed quite significant. The species IDs assumed by the Galaxy wrapper are (except for the first three, as you’ve already found @Anu ) all different from the ones here: [Chewie Nomenclature Server](https://chewbbaca.online/stats) I’ll clarify this with the developers of the wrapper. Thanks a lot for reporting, Wolfgang ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [April 8, 2026, 7:57pm UTC](https://help.galaxyproject.org/t/chewbbaca-downloadschema-schema-files-organisms-are-mixed-up/17638/4 "2026-04-08T19:57:06Z")
Reported here: [Chewbbaca DownloadSchema: Wrong species IDs assumed in wrapper · Issue #7868 · galaxyproject/tools-iuc · GitHub](https://github.com/galaxyproject/tools-iuc/issues/7868) ---
**Author:** ![Anu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/anu/32/8568_2.png) [@Anu](https://help.galaxyproject.org/u/Anu)\ **Post date:** [April 9, 2026, 8:51am UTC](https://help.galaxyproject.org/t/chewbbaca-downloadschema-schema-files-organisms-are-mixed-up/17638/5 "2026-04-09T08:51:12Z")
I’m fairly new to Galaxy and Bioinformatics, but I suspect this is the root of the problem (from the Chewie Nomenclature Server): ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/a/aaccbe31bd4a00ad0cfcfa5867f6a6819a9a1e13.png) So I guess the IDs are now mixed up, and the tool is probably grabbing the wrong schemes because of it. Thank you, Wolfgang, for reporting it on GitHub!