Installation of Qiime2 successful but can't activate due to inability in finding conda enviroment

[ngreenberg (Nathan Greenberg)]

Hi all,

I have been using Qiime2 for the past few months and have successfully created many outputs using newer versions of qiime2 such as (2022.2 and 2022.8). I installed these versions on my Windows PC using miniconda3 in Ubuntu 22.04.02 LTS. I have used them to run alpha and beta diversity analysis without any issues.

Recently I have been trying to use songbird (GitHub - biocore/songbird: Vanilla regression methods for microbiome differential abundance analysis) which only supports versions of QIIME 2 in between version 2019.7 and 2020.6. As such, I went to install one of these versions, Qiime2-2019.10, and am running into an issue that I have not experienced when installing other versions of conda using the same process.

To install qiime2, I first updated conda then I ran:
"wget https://data.qiime2.org/distro/core/qiime2-2019.10-py36-linux-conda.yml"
"conda env create -n qiime2-2019.10 --file qiime2-2019.10-py36-linux-conda.yml"

The conda env create line took a long time to process (approx 2 hrs) and it spit out a long list of things that can not all be included in this message. In the end I received this message:

As you can see I was not able to activate qiime2-2019.10 because the env was not discovered. As a bit of trouble shooting I tried looking at what environments were available:

I tried looking at the env list as well:

I checked the environment directory:

I also checked the conda configuration:

All of these checks seem to point to the correct environment where I was trying to install qiime2-2019.10 but it is not showing up anywhere. I have tried the same process with all version of qiime2 between 2019.7 and 2020.6 because I thought at first that the error might have been with the install of QIIME2 but I have not been able to activate any of the new environments.

I am assuming that the issue stems from sort of co-dependency with a newer version that I have already installed, but is there anything I am missing here? How should I go about installing a version of qiime2 that is needed for songbird?

Any and all help would be much appreciated. Thank you very much!

Thanks,
Nathan

[colinvwood (Colin Wood)]

Hello @ngreenberg,

It looks like your environment never got created because it never solved. The relevant info will be from the output you got just after executing

conda env create -n qiime2-2019.10 --file qiime2-2019.10-py36-linux-conda.yml

If you share more of this, we will be better able to troubleshoot.

[ngreenberg (Nathan Greenberg)]

Hi @colinvwood ,

Thank you very much for the quick response. As I mentioned above, there is so much code to share related to this so I didn't want to add all of it but here is some of the message I received:

There are multiple more pages of code output that I received that are not included in the above screenshots. Is there a better way to share this information with you?

Thank you,
Nathan

[colinvwood (Colin Wood)]

@ngreenberg,

Conda is finding conflicts for several packages. Don't worry about sifting through all the output, the import parts are e.g. Package liblapack conflicts for: (...)

You mentioned that you can use any qiime version between 2019.7 and 2020.6 to be compatible with another software package. The easiest next step is to just try to solve an environment with one of these other versions.

[ngreenberg (Nathan Greenberg)]

Hi @colinvwood ,

Thank you for this helpful information. I tried to install all four versions of QIIME2 that would be compatible with songbird (2019.7, 2019.10, 2020.2, and 2020.6). All four versions took about 2 hours to run and had numerous conflicts. In the end, none of them were able to be installed. All four versions gave this output at the end of running:

Is there any one package in particular that I could try adjusting to see if the installation process would work? It seems like there are so many that are occurring which is causing this issue.

Are the package conflicts likely occurring due to the newer versions of QIIME2 that already have installed? If so is there a way on Ubuntu to create another miniconda version to install and run this older version of QIIME2? Or are the package conflicts occurring due to trying to install these QIIME2 versions that are incompatible with the Ubuntu 22.04.02 LTS version?

Thank you,
Nathan

[colinvwood (Colin Wood)]

Hey @ngreenberg,

Run $conda config --show channel_priority and share the result, if possible.

Thanks.

[ngreenberg (Nathan Greenberg)]

Hi @colinvwood ,

Here is the output of what you requested:

Thanks,
Nathan

[colinvwood (Colin Wood)]

@ngreenberg,

Run $conda config --set channel_priority flexible then try solving one of those environments again.

[ngreenberg (Nathan Greenberg)]

Hi @colinvwood ,

That worked, thank you!! For my own understanding, why would the channel priority have been set to strict and why might changing it to flexible have solved this issue?

Best,
Nathan

[colinvwood (Colin Wood)]

@ngreenberg,

I don't know why your channel priority was set to strict. The default is flexible. As you saw, you can configure it manually, but I'm sure that there are ways that conda can change it behind the scenes too.

When the channel priority is set to strict, according to the docs:

Packages in lower priority channels are not considered if a package with the same name
appears in a higher priority channel.

I believe this means that conda won't let you get the versions of packages that you need to solve your environment from channels where they exist because it already found (an undesirable) version of the same package in a higher-priority channel.

Read the channel priority section of conda config --describe for more info.

Thanks.

[ngreenberg (Nathan Greenberg)]

Hi @colinvwood ,

Thank you very much for this information and for your help troubleshooting this issue!!

Best,
Nathan