Qiime2 Import 2025.10 errors: Standardize your fastq sequence names

usegalaxy.eu support
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Usegalaxy.eu has updated qiime2 to 2025.10, but this release has some problems with paired data affecting import and demux. Wondering if any fixes are on the horizon or if anyone is still running 2025.7.

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Hi @jln1137

Yes, the software package was updated. All of the prior versions are still hosted on the servers. This means you don’t need to upgrade your workflows or processes until you want to. Workflows will use the original tool versions included, and with direct use of the form you can navigate to the version you wish to use.

However, I’m curious about the error you are seeing. Would you like to troubleshooting this more? We did notice that the tool is stricter about the sample formatting.

This recommendation for the original sample formatting

.+_.+_L[0-9][0-9][0-9]_R[12]_001.fastq.gz

Now also seems to require that the values contained in .+ need to be a consistent character length for all in the same Qiime2 Import batch.

Meaning, a group like this will result in an error.

1_s1_L001_R1_001.fastq.gz
2_s2_L001_R1_001.fastq.gz
10_s10_L001_R1_001.fastq.gz

But padding out the values to all be the same character length like this works.

01_s01_L001_R1_001.fastq.gz
02_s02_L001_R1_001.fastq.gz
10_s10_L001_R1_001.fastq.gz

This was just noticed last Friday and I haven’t followed up on it more yet. So, I don’t know if this chnage was intentional or not yet, within the tool wrapper or what the remedy will be (possibly only updated documentation!). More soon about this. Update → Enhancement: clarify the element formats tighter specification NEW in qiime2_core__tools__import/2023.5.0+dist.h193f7cc9.3 · Issue #86 · qiime2/galaxy-tools · GitHub

Would you like to share your example, too, for troubleshooting? Or, maybe you noticed the same thing and this helps to come up with a reformatting strategy, if you want to use the updated version? How to get faster help with your question

Thanks and I hope this helps but please let us know if it actually does! :slight_smile:

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That works! Thank you.

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Great! Thanks for confirming! I’ll follow up with the developers about updating the guide on the form (and confirming this was all intentional). :rocket:

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@jennaj FYI for import from fastq there is now https://github.com/qiime2/galaxy-tools/blob/main/tools/suite_qiime2_core__tools/qiime2_core__tools__import_fastq.xml It allows to import from fastq in a more “Galaxy fashion”, i.e. from paired collections.

The tool is currently missing on usegalaxy.org

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Hi @bernt-matthias thanks for letting us know here! I now see the latest version from the tool shed at ORG now. Please let me know if I am not understanding this correctly.

Loading a list of pairs is so convenient!

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No, I mean https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2_core__tools__import_fastq/87623807fced

which is different from https://toolshed.g2.bx.psu.edu/view/q2d2/qiime2_core__tools__import/95475922280e

while the latter can be used to import all sorts of datatypes (and can be really difficult to use) the former one is specialized to the import of fastq data. The former one is missing on org.

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:partying_face: Updated method! FAQ: Create a Qiime2 qza artifact from a Galaxy collection in ONE STEP!