installation issue with qiime2-shotgun-2023.9

I have experienced installation issue with qiime2-shotgun-2023.9
please help me to resolve this issue.
Collecting package metadata (repodata.json): done
Solving environment: failed


  • gxx_impl_linux-64=13.2.0
  • libgomp=13.2.0
  • bracken=2.9
  • xcb-util-image=0.4.0
  • keyutils=1.6.1
  • xkeyboard-config=2.38
  • jack=1.9.22
  • libcups=2.3.3
  • alsa-lib=1.2.8
  • libsanitizer=13.2.0
  • libgcc-devel_linux-64=13.2.0
  • gfortran_impl_linux-64=13.2.0
  • attr=2.5.1
  • libstdcxx-ng=13.2.0
  • xcb-util=0.4.0
  • gcc_impl_linux-64=13.2.0
  • libnsl=2.0.0
  • libstdcxx-devel_linux-64=13.2.0
  • xcb-util-wm=0.4.1
  • libcap=2.66
  • xcb-util-keysyms=0.4.0
  • pulseaudio=16.1
  • libsystemd0=252
  • xcb-util-renderutil=0.3.9
  • libxkbcommon=1.5.0
  • _openmp_mutex=4.5
  • libgfortran-ng=13.2.0
  • libgcc-ng=13.2.0
  • libudev1=253
  • gridss=2.13.2

Hi @Sungwoo_Bae,
This was an issue that was occurring yesterday but it was fixed as of yesterday afternoon. Try reinstalling now! But remember to run this command before you try again:

rm qiime2-shotgun-2023.9-py38-osx-conda.yml


Thanks, it works now.

To "qiime" in on this topic...Is there a tutorial or are there specific instructions on how to use the qiime2-shotgun?

Hi @M_R,
qiime2-shotgun is in alpha release currently. Once the distribution is finalized there will be a tutorial.


Ah right. So, no chance for me to run it, unless I'm part of te development team? When is the beta and/or public release expected.

Thanks for the quick reply btw! :slight_smile:

Hi @M_R,

We do have install instructions on our user docs, and the install/usage process is very similar to the amplicon (formerly core) distribution. We've listed the available plugins associated with this distribution on our user docs as well, so you can see what plugins/tools are available in the alpha release. You can still test out and use this distribution, we just don't have the same guarantees as with the amplicon distribution. Feel free to run it and test things out!

Cheers :lizard:

1 Like

Don't forget about using --help and matching semantic types up, that will get you 99% of the way, although you will still need some familiarity of the broad-strokes for this kind of analysis.


I'll get some notes up in a forum post on how I've been using it in the next few days, and that can be a starting point for discussion about the workflow.


Hi @M_R,
I posted some information and a link to a draft tutorial here. Remember, this is early stage stuff - we'd love your feedback though!

Great! Many thanks! Will give it a go very soon!


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