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 1.2.0

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.

Prediction 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.
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 prediction 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 submitting a prediction 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.
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.
Benchmark Tag Navigation Error	When a prediction job is tagged with "benchmark_" followed by an ID (e.g., "benchmark_123"), clicking the tag on the result details page incorrectly attempts to load a benchmark with that ID, resulting in a "benchmark not found" error.	Avoid using tags that start with "benchmark_" for regular prediction jobs.
Input Assets Not Recovered from Previous Jobs	When using the "Previous" button or similar navigation to recover inputs from previous jobs, input assets (uploaded files) are not recovered.	Manually re-upload the required input assets when reusing previous job configurations.
Model Parameters Not Reset on Model Change	When selecting a model on the prediction form and then changing to a different model, the model parameters are not automatically reset to the defaults of the newly selected model.	Click the "Defaults" button after changing models to ensure correct default parameters are applied. This issue does not affect the benchmark tab.
Form Submission Blocked After MSA Server Switch	On the benchmark form, switching to the MSA server configuration to change the active server and then returning to the form can block submission with a "Could not validate, the schema is missing" error on model parameters.	Avoid switching MSA servers after loading a benchmark form, or reload the benchmark form after making MSA server changes.
Benchmark MSA Validation Blocked by Invalid Files	When uploading multiple CIF files to a benchmark, if one file is invalid, MSA server validation is blocked for all files, including valid ones.	Ensure all uploaded CIF files are valid before submitting. Validation should ideally process valid files independently, but currently all files must be valid for MSA validation to proceed.
Example Files Added Multiple Times	When clicking on a benchmark example multiple times rapidly, the example files can be added to the form multiple times instead of just once.	Click the example button only once and wait for the files to load.
Empty Sequence Validation Only in JSON Tab	When adding a new query entry using the query builder, empty sequence validation errors only appear in the JSON tab, not in the query builder interface itself.	Check the JSON tab to see validation errors for empty sequences when using the query builder.

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.
Bash Version Check Missing in Deploy Script	The deploy_apherisfold script requires GNU Bash version 4.0 or higher but does not check this requirement before execution. Running the script with an older version or a different shell results in cryptic error messages.	Ensure you are using GNU Bash version 4.0 or higher before running the deployment script. Verify your bash version with bash --version.