Could not find the "--resample 100" option for fel mode?

[liamxg]

Available analysis command line options

Use --option VALUE syntax to invoke
If a [reqired] option is not provided on the command line, the analysis will prompt for its value
[conditionally required] options may or not be required based on the values of other options

code
Which genetic code should be used
default value: Universal

alignment [required]
An in-frame codon alignment in one of the formats supported by HyPhy

tree [conditionally required]
A phylogenetic tree (optionally annotated with {})
applies to: Please select a tree file for the data:

branches
Branches to test
default value: All

srv
Include synonymous rate variation in the model
default value: Yes

pvalue
The p-value threshold to use when testing for selection
default value: 0.1

output
Write the resulting JSON to this file (default is to save to the same path as the alignment file + 'FEL.json')
default value: fel.codon_data_info[terms.json.json] [computed at run time]

precision
Optimization precision settings for preliminary fits
default value: standard

full-model
Perform branch length re-optimization under the full codon model
default value: Yes

[liamxg]

@spond @aglucaci

[liamxg]

and also no option for --ci Yes.

[aglucaci]

Hello @liamxg, which version of HyPhy are you using? I suggest installing the latest version as some features may not be supported in older versions. I do see the resample and ci keywords in the current version of FEL.

Best,
Alexander

[liamxg]

@aglucaci mine is v2.5.48? what is the latest version?

[stephenshank]

Dear @liamxg,

You can track releases here. The latest is 2.5.57.

Just FYI, if you are a conda user there are some install issues that will need to be troubleshot to get the latest version. I will look into this today, and there is always the option to install with CMake.

Thanks for all of the activity on our Github! Feedback from our users is extremely helpful.

Regards,
Stephen

[liamxg]

@stephenshank thanks for your help, how to use CMake to install the latest version?
Is there any other ways to install the latest version?

[spond]

Dear @liamxg,

How did you install the version you currently have?

Best,
Sergei

[liamxg]

Dear @spond using conda install -c bioconda hyphy, if I am not mistaken.

[liamxg]

@stephenshank @spond the develop version is 2.5.58, right?

[stephenshank]

Dear @liamxg,

I've pushed OSX and Linux builds to my conda channel that I am now testing. I should have a temporary fix for you soon and a fix for the remainder of our users soon after. Thanks again for reporting this, we were unaware that our automated release process had broken.

develop will contain cutting/bleeding edge features and could be in a constant state of flux depending on what someone is working on. It is technically not the same as 2.5.58 because that release has not occurred yet, and develop may undergo more feature development and bug fixes before that happens. We (loosely) adhere to semantic versioning and git flow in our development process.

Regards,
Stephen

[stephenshank]

@liamxg I've now verified that hyphy and HYPHYMPI analyses run on both arm64 and x86_64. Can you please try using my conda channel, either

conda create -n hyphy2557 -c stephenshank hyphy=2.5.57

if you are creating a new environment, or

conda install -c stephenshank hyphy=2.5.57

if you are adding to an existing environment. Please try both if one fails.

You can verify the installation with hyphy --version, which should yield something like

HYPHY 2.5.57(MP) for Linux on $YOUR_ARCH

Using my channel is a temporary fix. I need to submit a pull request to bioconda that works and gets merged which is somewhat out of my control, but this should hopefully get you up and running ASAP.

[liamxg]

Dear @stephenshank still not work:

(base) simon@192 selection-tutorial % conda install -c stephenshank hyphy=2.5.57
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• hyphy=2.5.57

Current channels:

• https://conda.anaconda.org/stephenshank/osx-64
• https://conda.anaconda.org/stephenshank/noarch
• https://conda.anaconda.org/conda-forge/osx-64
• https://conda.anaconda.org/conda-forge/noarch
• https://conda.anaconda.org/bioconda/osx-64
• https://conda.anaconda.org/bioconda/noarch
• https://repo.anaconda.com/pkgs/main/osx-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/osx-64
• https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(base) simon@192 selection-tutorial % hyphy --version
HYPHY 2.5.48(MP) for Darwin on x86_64

[stephenshank]

Dear @liamxg,

Thank you for trying the commands, it's really helpful to hear from our users!

It appears as though you are on an Intel-based Mac, based on this correspondence and the output HYPHY 2.5.48(MP) for Darwin on x86_64 above.

When time permits, I will try to perform a build for that target on AWS.

Regards,
Stephen

[liamxg]

Dear @stephenshank you are so nice.

[stephenshank]

Thanks @liamxg, you are as well! I cannot emphasize it enough: feedback from our users is such a critical part of our process.

For example, your comment prompted some maintenance of our bioconda packaging, which is responsible for 100,000 downloads of our software.

So you have my sincere gratitude.

[liamxg]

Dear @stephenshank you are so nice. Hope I can work with you.

[stephenshank]

Dear @liamxg,

Thanks to your inquiry we now have a HyPhy 2.5.57 release on bioconda. Can you please try installing with your normal procedure? Please let me know if you encounter any issues.

Regards,
Stephen

[liamxg]

Dear @stephenshank,

thanks. But still not work:

• urllib3 -> pysocks[version='>=1.5.6,<2.0,!=1.5.7'] -> __win

Your installed version is: 13.4

Note that strict channel priority may have removed packages required for satisfiability.

(base) simon@192 ~ % hyphy --version
HYPHY 2.5.48(MP) for Darwin on x86_64

[stephenshank]

Dear @liamxg,

I'm not sure why you're encountering this issue. I was just able to install on an Intel-based Mac.

For what it's worth I use Miniconda. You'll also need to ensure that you have Bioconda set up. Also, my conda verison is 23.10.0; if yours is 13.4, it could be a bit out of date.

If you want to continue with this approach, can you please try in a newly installed Miniconda that is configured for Bioconda?

Regards,
Stephen

[liamxg]

Dear @stephenshank ,
my conda version: 23.7.4
(base) simon@192 ~ % conda --version
conda 23.7.4