Apheris Hub - Known Issues

Below, we list known issues with Apheris Hub. If available, we list a workaround to help troubleshoot the issue.

This list will be constantly evolving with input from our different users and with the evolution of our product in future releases.

Known Issues with Apheris Hub 1.1.0

OpenFold3

Issue	Description	Additional information
Unexpected Behavior on some Batch Requests	Due to an unresolved MSA cache bug in the OpenFold3 code base, batch requests (i.e. requests with more than one query) with more than a single unique protein sequence and counterpart MSA may cause unexpected behavior.	Please submit individual requests with a single query for these complexes.
MSA Files Cannot Be Used with OpenFold3	An issue prevents the reliable usage of MSA files with the current OpenFold3 model.	Do not use MSA files with the OpenFold3 model version. The public MSA server version is available, but you should not use MSA files with it.

Inference and Processing

Issue	Description	Additional information
ColabFold Server Rate Limiting	The public ColabFold server applies rate limiting, which can significantly slow down processing of even simple queries.	If you encounter slower than anticipated query times it is likely due to using the public ColabFold server. Please wait a few minutes and try again or use MSAs from file if the model supports it.
Request Status Tracking	Inference requests can get stuck in a "running" state if the corresponding model is stopped or uninstalled during processing.	After an instance restart, the request is transitioned to done, but the results are not displayed.
Results Polling	When going to the results page before a prediction completed, you might have to refresh the page for the results to load.
Delayed Execution on Shared GPU	When we have a single GPU being shared between two running model versions, parallel jobs can be started on each of those models. However, because they share the same GPU, the execution can be blocked and delayed.	Additionally, the UI shows the delayed requests as "Running" instead of "Pending", as they are waiting for the GPU to become available.
Error Log Display	Error logs are shown even for successful inference runs. However, they don't always contain errors per se but just the stderr output.
Job Duration Metrics	Job duration doesn't distinguish between waiting time and actual running time, which can be misleading when multiple jobs are queued.
No validation that MSA file sequence and sequence provided in queries match	Queries containing unknown residues (X character) at the beginning of sequences, particularly when combined with ligands like HEM, may cause MSA generation errors.	Apheris will during next releases improve the validations being performed before a user submiting an inference run we know will fail.
Nonstandard residues between parentheses are not support	Including nonstandard residues in parentheses causes the MSA to crash. Generally, these should be converted to X before sending to an MSA server	Apheris will during next releases add support for Nonstandard residues.

Security

Issue	Description	Additional information
Container User Privileges	Docker containers are currently running with root user privileges, which is not a security best practice.

User Interface

Issue	Description	Additional information
PAE/PDE Plot Selection	When trying to select areas of the PAE/PDE plot, the selection box behaves erratically and lower areas cannot be selected. It is not possible to highlight the edges of the plot.
Empty Models Section with Wrong API Key	When installing a model with an incorrectly set API key, the home page displays an empty "Your models" section and progress bars are shown.
API Documentation Error for Support Endpoint	The API documentation shows an error when viewing the GET /api/v1/support/zip endpoint.
PAE Filter Issues on Window Resize	When resizing the browser window or zooming out while viewing results, the PAE filter selection may appear and disappear unexpectedly. Clicking deselect may not work consistently.	If you experience this issue, try avoiding window resize operations while working with PAE plots.

Installation and Configuration

Issue	Description	Additional information
Port Allocation	The installation script uses a fixed port (8080) which may already be in use on some systems.	As a workaround, ensure port 8080 is available before installation or modify the port in the installation script.
Inconsistent Access Key / API Keys Formats in k8s deployment guide	The Kubernetes deployment guide use different input formats for keys that need to be provived (e.g.: key used to access Apheris Hub Applications is in a username:password format while key for MSA Server configuration is base64 encoded) which can cause confusion during deployment.	In the future we aim to simply use the base64 encoded version and enable the chart to deal with the decoding
Single GPU Limitation with Multiple Models	When deploying the Hub using Kubernetes and Helm on a machine with only one GPU, only one model (OpenFold3 or Boltz-2) can be started at a time.	Use a machine with multiple GPUs, enable fractional GPU usage, or run one model at a time. This limitation should be considered when planning your deployment infrastructure.

Documentation

| Issue | Description | Additional information | | Outdated references to old Hub architecture | Documentation still contains references to the previous Hub architecture: Model installations, Model management, Configuration examples | We will issue a patch release in the next couple of days covering the changes needed to the documentation | [//]: # (EN-4474) | Missing documentation for Model Weights selection | Documentation that explains how a user can select between multiple Model Weights (whey they are provided by a given model) was not yet included. | We will issue a patch release in the next couple of days with a new documentation section for this feature. | [//]: # (EN-4265)