Asking about qiime2 tools import

usegalaxy.org support
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2

Welcome @Gehad_Abdelsattar_Mo

Hopefully you found this help already and solved the problem, but if not I’ll link it here:

In short, the data organization needs to follow these guidelines

  1. Reads are in a list collection folder. Both forward and reverse reads, together in a single list. This is different from other tools that handle paired end data in Galaxy where a paired collection folder is often used.
  • The sequence reads must be named with their original format from off the sequencer. This is parsed by the Qiime2 Import tools, and is a common place where errors occur. The tool form has details about the expected file names and these can be adjusted in Galaxy. Most of the topics under qiime2_core__tools__import are discussions about this.
  1. Provide the additional metadata files as needed.
  • Varies by tool. Paying attention to the tabular format is important. Files with stray spaces or tabs can be “cleaned up” with Text Manipulation tools that replace spaces in labels with underscores or collapse multiple tabs into one.
  1. Refer to the Qiime2 user guides for file format specifications.
  • These can get quite complicated depending on the data, but the file format/content (what is inside the files) in Galaxy will always be the same as when the tools are used directly. The only Galaxy difference is with external metadata: how the datatype format label is assigned and how the files are originally organized (collection folders). Xref → QIIME 2 Library

I hope this provides some context for you or anyone else reading later on. If this is still a problem, you are welcome to share back your history in a reply, and we can help to get your data imported. What to do exactly depends on what you have now, so it is hard to guess without seeing the data organization, how it labeled, form parameters, metadata files, and the full error produced so far. A shared history provides all of that in a single link and you can unshare after we are done. How to: How to get faster help with your question :slight_smile: