# Qimme2 tools import issue **URL:** \ **Category:** usegalaxy.org support\ **Tags:** collections, tool-help, collection-shape\ **Created:** [October 17, 2025, 10:37am UTC](https://help.galaxyproject.org/t/qimme2-tools-import-issue/16406 "2025-10-17T10:37:41Z")\ **Posts on this page:** 1\ **Showing post:** 2
**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:** [October 17, 2025, 7:04pm UTC](https://help.galaxyproject.org/t/qimme2-tools-import-issue/16406/2 "2025-10-17T19:04:48Z")
Welcome @Eirecantinaband The **Qiime2 Import** tool will require the original full Illumina file names. Why? The tool does some parsing internally to organize the artifact. > [@Qiime2 import troubleshooting: Retain original Illumnia file names + use simple list collection](https://help.galaxyproject.org/t/qiime2-import-troubleshooting-retain-original-illumnia-file-names-use-simple-list-collection/15889/3): > > the solution is to retain the full original Illumina sequence names for the collection identifiers and to put both forward and reverse reads together in a simple β€œlist” collection. The collection builder tool will suggest a paired collection shape but you can toggle to the list shape instead. πŸš€ How to do this: 1. Load the reads up to your Galaxy history with the **original file names** intact. 2. Create a **list collection** using all default settings: **History gear menu β†’ Auto Build List** 3. Load the data into the **Qimme2 Import** tool. More details and resources are in this topic. β†’ [Asking about qiime2 tools import](https://help.galaxyproject.org/t/asking-about-qiime2-tools-import/15795) And at the Qiime2 website here β†’ [How to import data for use with QIIME 2 - Microbiome marker gene analysis with QIIME 2](https://amplicon-docs.qiime2.org/en/latest/how-to-guides/how-to-import.html). The command line tools will work about the same in Galaxy so the original guides are useful to learn what is going on inside of the artifacts, and how the artifacts are originally constructed, and why certain data information (such as the full sequence and file names) are important. So, for the issue here, the problem was likely the file names. > [@Eirecantinaband](#): > > They are filename.effective.fastq.gz and filename.fna.gz. And, for your question here, you could explore other tool suites? Our tutorials include workflows, too, that could be customized. > [@Eirecantinaband](#): > > Firstly, I don’t know which is best for me to analyse? The Qimme2 tools can be a bit complicated due to the artifact data structures, instead of the native data collection folder formats usually used in Galaxy. This tutorial category at the πŸŽ“ **GTN Training** site contains appropriate analysis examples for your data. β†’ [Microbiome / Tutorial List](https://training.galaxyproject.org/training-material/topics/microbiome/) Or, you can explore with a search term like this β†’ [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=16s) (query=16s) This would be a good place to start! > **[Microbiome / 16S Microbial Analysis with mothur (short) / Hands-on: 16S...](https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html)** > > A microbiome is the community of microorganisms that can usually be found living together in any given habitat. Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume... * * * Most of these complete analysis pathways will require more than a single sample and a single reference sequence, but you can explore. Maybe some of the tools can be used independently to get you the information you want? You’ll need to review to see if these will work for your goals. Hope this helps! πŸ™‚ --- _[View the full topic](https://help.galaxyproject.org/t/qimme2-tools-import-issue/16406)._