Troubleshooting

Julia executable was not found

Install Julia from https://julialang.org/downloads/ or pass an explicit path:

from admixture import OpenAdmixtureRunner

runner = OpenAdmixtureRunner(julia="/path/to/julia")

OpenADMIXTURE.jl is not installed

Instantiate the packaged Julia project:

admixture setup

PLINK files are missing or empty

For bfile="data/example", all three files must exist and be non-empty:

data/example.bed
data/example.bim
data/example.fam

Output files are missing

The wrapper looks for common output names such as:

<out_prefix>.Q
<out_prefix>.P
<out_prefix>.log
<out_prefix>.<K>.Q
<out_prefix>.<K>.P
<out_prefix>_K<K>.Q
<out_prefix>_K<K>.P

If multiple .Q files match, remove stale files or choose a unique out_prefix.

Paths with spaces

Paths with spaces are supported because the runner passes a list of subprocess arguments and uses shell=False. If you see path issues, include result.command or the raised exception text in your bug report.

OpenADMIXTURE runtime test prerequisites

Runtime tests require Julia and OpenADMIXTURE.jl. They should fail, not skip, if either is unavailable:

pytest tests

The malariagen-data compatibility test skips only on Python 3.13+ because malariagen-data is unavailable there. Default tests do not read from Google Cloud Storage.

If you run manual experiments against real MalariaGEN data on Google Cloud Storage, you need access to the relevant bucket and Google Cloud Application Default Credentials:

makim gcloud.auth

For non-interactive local runs with a service-account JSON key, export:

export GOOGLE_APPLICATION_CREDENTIALS=/path/to/service-account.json

In GitHub Actions, a service-account JSON key can be provided in the GOOGLE_CREDENTIALS repository secret for workflows that need real MalariaGEN-GCS access. The service account must have access to the relevant bucket. Do not use a Google API key; API keys do not provide the Application Default Credentials expected by malariagen-data.