Cannot install qiime in ubuntu24.04, staying on executing transaction in hours

Technical Support
1

I am trying to install QIIME2 in Ubuntu24.04 but it always stay in state of "executing transaction" after inputting 'conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml', it proceeds to run for hours and fails to finish install. What is the matter with that?

The error information as follows:

conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml
Channels:

  • released
  • conda-forge
  • bioconda
  • defaults
    Platform: linux-64
    Collecting package metadata (repodata.json): done
    Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: -
/ done
ERROR conda.core.link:_execute(938): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.11-r43hdfd78af_1'.
Rolling back transaction: done

CondaSignalInterrupt: Signal interrupt SIGINT
()

2

Hello @yawei,

Welcome to the forums!

Thank you for sharing your full error message.

It looked like everything went well, except that one package.

There are lots of forum posts about genomeinfodbdata failing to install.
If I got this error, I would simply run it again and hope the R database links this time.

1 Like
3

Thanks for your reply and help!

To better understand the issue, I have tried to installation many times, and I find that the package "genomeinfodbdata-1.2.11" could not downloaded, even though I using the other downloading tools foe example browser. Is any solution for me please?

Thanks in advance again!

1 Like
5

Hello,

Did you try to clean the conda before installation?

conda clean - -all

I would also try to update conda by:

conda update -n base -c defaults conda

Best,

6

Hi， @timanix

Thanks for your reply, I have tried to install Qiime2 according to your method, but it is didn't work for me. I have also tried many other methods, too, but always get an error. Maybe I should wait for the lastest version of qiime2.

Thanks for your help anyway!

Best,

10

Hello!
Did you manage to solve the issue?
I just got a hint from @SoilRotifer that you need to check the channel priority:

conda config --describe channel_priority

If it is set to "strict", then change it to "flexible".

conda config --set channel_priority flexible

Please share with us if you already solved the issue and if yes, then how. If not, then try the commands above and give us the feedback.

Best,
Timur

12

Hello， @ timanix

Thanks for your reply! The channel priority was already set to "flexible", while it didn't work for me.
.
By the way, I tried to install "genomeinfodbdata-1.2.11" alone using both conda and local installation methods, but it alway got an error.

Thanks for you help anyway!

Best wishes!

1 Like
14

Hi @yawei,

It may be worth attempting to re-install your instance of conda (or miniconda), just to try starting from a clean slate. Before we do that, can you please run conda env list and provide the output in your reply?