I'd like to use the dbotu_q2 plugin with my amplicon sequencing data. The commands to install the plugin as recommended in the qiime2 library and Anaconda.org (below) both execute successfully:
Error: QIIME 2 has no plugin/command named 'dbotu-q2'.
I'm trying to install into a qiime2-amplicon-2024.2 conda environment but I've tried installing into other environments and run into the same problem. I also tried downloading and executing via the GitHub repo but this broke the entire conda environment until I removed the package. Not sure if I'm downloading into the wrong place or have incompatibilities. Any help would be greatly appreciated.
Hi @Oryx-scimitar,
Have you run qiime dev refresh-cache? Your current QIIME 2 environment might be cached and therefore doesn't know about your new plugin?
Additionally I am not sure if these plugin is compatible with our new release of qiime2. You may want to try a different qiime2 release!
Success...followed by a new challenge! Refreshing the cache didn't help but installing qiime2-2019.10 enabled me to install the dbotu_q2 plugin (this involved some trial and error as I started trying earlier versions of Qiime2 mentioned in the plugin info but there were lots of package conflicts when I tried to install them with conda). Thanks @cherman2 so much for this suggestion.
The plugin is now installed and running but unfortunately it doesn't recognise the artifacts I've created in qiime2-amplicon-2024.2.
ValueError: results/AnEh_ASVs.qza was created by 'QIIME 2024.2.0'. The currently installed framework cannot interpret archive version '6'
I'm reliant on some more recent plugins to create these files so don't think I can go back and run my data through the older qiime release. I'll see if I can find any guidance on the forum to deal with this new issue. Any advice welcome.
However, we updated our file format and past releases don't know how to process this new format.
I definitely understand this is not ideal but the only way to use dbotu_q2 plugin in our amplicon distro is to use an older release from start to finish.
Another option might be to try installing this community plugin in our tiny distro. tiny-distro install guide.
This is our tiniest distro (therefore less dependencies to mess up the install). you might be able to install the dbotu_q2 plugin in the tiny distro. Hopefully we can get dbotu_q2 installed here and therefore avoid this error:
ValueError: results/AnEh_ASVs.qzv was created by 'QIIME 2024.2.0'. The currently installed framework cannot interpret archive version '6'
I have already tried installing it in the 2024.2 tiny distro and it ran into the same issue as trying to install in the 2024.2 amplicon distro i.e. it appears to install but won't run. What a shame.
Fortunately, I've managed to get the dbotu3 pipeline running directly in Linux. I think it makes more sense for me to do this, then import the outputs to the current version of qiime, rather than trying to rerun my entire pipeline through an outdated version of qiime.
Thanks for your help @cherman2. Perhaps some notes re using this plugin could be added in the document library so that other users are aware of these issues. I don't get the impression it's a heavily used plugin though as not much came up when I tried to troubleshoot the incompatibilities.